modified other distance measurements (like for temperature coefficient) (08b36456) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+116 −22

Original line number	Diff line number	Diff line
		@@ -46,6 +46,7 @@ import java.util.regex.Matcher;
		import java.util.regex.Pattern;



		//import FocusingField.FocusingFieldMeasurement;
		//import FocusingField.MeasuredSample;
		import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/
		@@ -4388,6 +4389,7 @@ if (MORE_BUTTONS) {
		String path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+"-focus.csv";
		if (MASTER_DEBUG_LEVEL>0) System.out.println ("Saving focusing log data to "+path);
		MOTORS.listHistory(
		FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD!=null),
		path, // on screen, path - to csv
		FOCUS_MEASUREMENT_PARAMETERS.lensSerial,
		FOCUS_MEASUREMENT_PARAMETERS.comment,
		@@ -4473,6 +4475,7 @@ if (MORE_BUTTONS) {
		if (label.equals("List History")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		MOTORS.listHistory(
		FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD!=null),
		null, // on screen, path - to csv
		FOCUS_MEASUREMENT_PARAMETERS.lensSerial,
		FOCUS_MEASUREMENT_PARAMETERS.comment,
		@@ -5268,7 +5271,7 @@ if (MORE_BUTTONS) {
		checkSerialAndRestore(); // returns true if did not change or was restored
		boolean modeAverage=label.equals("Focus Average");
		boolean noTiltScan=true;
		boolean useLMA=true;
		// boolean useLMA=true;
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
		FOCUS_MEASUREMENT_PARAMETERS,
		@@ -5285,7 +5288,8 @@ if (MORE_BUTTONS) {
		}
		gd.addCheckbox("Erase previous measurement history",modeAverage);
		gd.addCheckbox("Allow tilt scan when looking for the best fit",!noTiltScan);
		gd.addCheckbox("Use LMA calculations for focus/tilt",useLMA);
		gd.addCheckbox ("Use lens aberration model (if available) for focal distance and tilts", FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics);
		// gd.addCheckbox("Use LMA calculations for focus/tilt",useLMA);
		double scanMinutes=modeAverage?2.0:30.0;
		gd.addNumericField("Measure for ", scanMinutes , 1,5," minutes");
		gd.showDialog();
		@@ -5297,7 +5301,17 @@ if (MORE_BUTTONS) {
		}
		if (gd.getNextBoolean()) MOTORS.clearHistory();
		noTiltScan=!gd.getNextBoolean();
		useLMA=gd.getNextBoolean();
		FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics=gd.getNextBoolean();
		// Only try to read history if useLMAMetrics is set
		if (FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD==null)) {
		if (DEBUG_LEVEL>0) System.out.println("FOCUSING_FIELD==null, trying to restore from the previously saved file");
		if (!restoreFocusingHistory(false)) { // try to restore from the saved history file
		System.out.println("Failed to restore history, disabling use of lens aberration model");
		}
		FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
		}
		boolean useLMA=FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD!=null);

		// int startHistPos=MOTORS.historySize();
		scanMinutes=gd.getNextNumber();
		long startTime=System.nanoTime();
		@@ -5319,6 +5333,14 @@ if (MORE_BUTTONS) {
		pX0,
		pY0);
		}
		if (useLMA){
		FOCUSING_FIELD.testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
		if (MASTER_DEBUG_LEVEL>0) {
		System.out.println("Optimal absolute Zc="+FOCUSING_FIELD.qualBOptimizationResults[0]);
		System.out.println("Optimal Tx="+FOCUSING_FIELD.qualBOptimizationResults[1]);
		System.out.println("Optimal Ty="+FOCUSING_FIELD.qualBOptimizationResults[2]);
		}
		}
		while (System.nanoTime()<endTime){
		moveAndMaybeProbe(
		true, // just move, not probe
		@@ -5350,7 +5372,6 @@ if (MORE_BUTTONS) {

		}
		// LMA version

		FocusingField ff= null;
		if (useLMA){
		ff= new FocusingField(
		@@ -5371,22 +5392,34 @@ if (MORE_BUTTONS) {
		ff,
		(runs==0)?0:(MOTORS.historySize()-runs),
		MOTORS.historySize()); // all newly acquired
		// TODO: Remove after checking average
		/*
		if (modeAverage && (FOCUSING_FIELD!=null)){ // calculate/show average over the last run - only in "average" mode
		double [] ZTM=FOCUSING_FIELD.averageZTM(noTiltScan,ff); // no tilt scan - faster
		double [] ZTM=FOCUSING_FIELD.averageZTM(
		noTiltScan,
		ff, // no tilt scan - faster
		true); // noMotors
		if (MASTER_DEBUG_LEVEL>0) {
		String msg="Failed to calulate average focus/tilt";
		if (ZTM!=null) msg="Average:\n"+
		if (ZTM!=null) {
		msg="Average:\n"+
		"Relative focal shift "+IJ.d2s(ZTM[0],3)+"um (absolute - "+IJ.d2s(ZTM[0]+FOCUSING_FIELD.qualBOptimizationResults[0],3)+"um)\n"+
		"Relative horizontal tilt "+IJ.d2s(ZTM[1],3)+"um/mm (absolute - "+IJ.d2s(ZTM[1]+FOCUSING_FIELD.qualBOptimizationResults[1],3)+"um.mm)\n"+
		"Relative vertical tilt "+IJ.d2s(ZTM[2],3)+"um/mm (absolute - "+IJ.d2s(ZTM[2]+FOCUSING_FIELD.qualBOptimizationResults[2],3)+"um.mm)\n"+
		"Suggested M1 "+IJ.d2s(ZTM[3],0)+"steps\n"+
		"Relative vertical tilt "+IJ.d2s(ZTM[2],3)+"um/mm (absolute - "+IJ.d2s(ZTM[2]+FOCUSING_FIELD.qualBOptimizationResults[2],3)+"um.mm)\n";
		if (ZTM.length>3) {
		msg+="Suggested M1 "+IJ.d2s(ZTM[3],0)+"steps\n"+
		"Suggested M2 "+IJ.d2s(ZTM[4],0)+"steps\n"+
		"Suggested M3 "+IJ.d2s(ZTM[5],0)+"steps";
		}
		}
		System.out.println(msg);
		IJ.showMessage(msg);
		}
		}
		*/
		//
		}

		if (FOCUS_MEASUREMENT_PARAMETERS.saveResults) {
		String dir=getResultsPath(FOCUS_MEASUREMENT_PARAMETERS);
		File dFile=new File(dir);
		@@ -5415,6 +5448,7 @@ if (MORE_BUTTONS) {
		sensorHeight=FOCUSING_FIELD.sensorHeight;
		}
		MOTORS.listHistory(
		useLMA,
		path, // on screen, path - to csv
		FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
		FOCUS_MEASUREMENT_PARAMETERS.lensSerial,
		@@ -5442,11 +5476,13 @@ if (MORE_BUTTONS) {
		if (!modeAverage) {

		double [] lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
		useLMA,
		runs, // number of last samples from history to use, 0 - use all
		FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightK,
		FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightY
		);
		double [] allKT=MOTORS.focusingHistory.temperatureLinearApproximation(
		useLMA,
		0, // number of last samples from history to use, 0 - use all
		FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightK,
		FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightY
		@@ -5467,6 +5503,7 @@ if (MORE_BUTTONS) {
		IJ.showMessage("Info",msg);
		}
		// Now in LMA mode - recalculate and overwrite
		/*
		if (useLMA){
		ff= new FocusingField(
		EYESIS_CAMERA_PARAMETERS.getSensorWidth(),
		@@ -5486,7 +5523,12 @@ if (MORE_BUTTONS) {
		if (MASTER_DEBUG_LEVEL>0){
		System.out.println ("* Calculating focal distance shift for each of "+MOTORS.historySize()+" recorded measurments *");
		}
		double [][] allZTM=FOCUSING_FIELD.getAllZTM(noTiltScan,ff); // no tilt scan (supposed to be adjusted
		boolean noMotors=true;
		double [][] allZTM=FOCUSING_FIELD.getAllZTM(
		noTiltScan,
		ff, // no tilt scan (supposed to be adjusted
		noMotors); // boolean noMotors) // do not calculate correction

		lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
		allZTM,
		runs
		@@ -5511,6 +5553,7 @@ if (MORE_BUTTONS) {
		IJ.showMessage("Info",msg);
		}
		}
		*/
		}
		saveCurrentConfig();
		return;
		@@ -9125,6 +9168,12 @@ if (MORE_BUTTONS) {
		double [][][] sampleCoord=null;
		if (FOCUSING_FIELD!=null){
		sampleCoord=FOCUSING_FIELD.getSampleCoord();
		FOCUSING_FIELD.testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
		if (MASTER_DEBUG_LEVEL>0) {
		System.out.println("Optimal absolute Zc="+FOCUSING_FIELD.qualBOptimizationResults[0]);
		System.out.println("Optimal Tx="+FOCUSING_FIELD.qualBOptimizationResults[1]);
		System.out.println("Optimal Ty="+FOCUSING_FIELD.qualBOptimizationResults[2]);
		}
		} else {
		sampleCoord=FOCUS_MEASUREMENT_PARAMETERS.sampleCoordinates(
		FOCUS_MEASUREMENT_PARAMETERS.result_PX0,
		@@ -9154,7 +9203,12 @@ if (MORE_BUTTONS) {
		//get measurement
		FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);
		// calculate z, tx, ty, m1,m2,m3
		double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(false,fFMeasurement,false); // allow tilt scan
		double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(
		false, // allow tilt scan
		fFMeasurement,
		false, // parallel move
		true, // boolean noQualB, // do not re-claculate testQualB
		false); // boolean noAdjust); // do not calculate correction
		// show dialog: Apply, re-calculate, exit
		int [] currentMotors=fFMeasurement.motors;
		int [] newMotors=currentMotors.clone();
		@@ -9279,7 +9333,13 @@ if (MORE_BUTTONS) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
		if (parallelMove){ // ignore/recalculate newMotors data
		zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(false,fFMeasurement,true); // recalculate with parallel move only, allow tilt scan
		zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(
		false,// disable tilt scan
		fFMeasurement,
		true, // recalculate with parallel move only
		false, // boolean noQualB, // do not re-claculate testQualB - OPTIMIZE to do once
		false); // boolean noAdjust); // do not calculate correction

		newMotors=currentMotors.clone();
		if (zTxTyM1M2M3!=null){
		newMotors[0]=(int) Math.round(zTxTyM1M2M3[3]);
		@@ -11114,6 +11174,34 @@ if (MORE_BUTTONS) {
		debugLevel,
		loopDebugLevel);
		// System.out.println(">>"+focusingMotors.historySize()+": "+focusingMotors.curpos[0]+", "+focusingMotors.curpos[1]+", "+focusingMotors.curpos[2]);
		int ca=6;
		double [] zTxTy=null; // {Double.NaN,Double.NaN,Double.NaN};
		double oldTx=Double.NaN,oldTy=Double.NaN,oldFarNear=Double.NaN;
		if (metrics!=null ){
		oldFarNear=metrics[ca][0];
		oldTx= metrics[ca][1];
		oldTy= metrics[ca][2];
		}
		if (FOCUS_MEASUREMENT_PARAMETERS.useLMAMetrics && (FOCUSING_FIELD!=null)){
		FocusingField.FocusingFieldMeasurement fFMeasurement= FOCUSING_FIELD.getFocusingFieldMeasurement(
		ts, //focusingState.getTimestamp(),
		focusMeasurementParameters.sensorTemperature,
		focusingMotors.readElphel10364Motors(), //focusingHistory.getPosition(), //null?
		rFullResults[0]); //focusingState.getSamples());

		zTxTy=FOCUSING_FIELD.adjustLMA(
		true, // false, // noTiltScan
		fFMeasurement,
		false, // parallel move
		true, // boolean noQualB, // do not re-claculate testQualB
		true); // boolean noAdjust); // do not calculate correction
		if (zTxTy!=null){
		metrics[ca][0]=zTxTy[0]; // was far/near
		metrics[ca][1]=zTxTy[1];
		metrics[ca][2]=zTxTy[2];
		}

		}

		focusingMotors.addToHistory(ts,focusMeasurementParameters.sensorTemperature,metrics,rFullResults[0]);
		// System.out.println("focusMeasurementParameters.lensDistanceWeightK="+focusMeasurementParameters.lensDistanceWeightK);
		@@ -11121,7 +11209,7 @@ if (MORE_BUTTONS) {
		if ((debugLevel>0) && (metrics!=null)){
		// see if lens is calibrated
		double [] resolutions={1.0/metrics[1][6],1.0/metrics[5][6],1.0/metrics[2][6]}; // R,G,B
		double fDistance=focusingMotors.focusingHistory.getLensDistance(
		double fDistanceOld=focusingMotors.focusingHistory.getLensDistance(
		resolutions, // {R-sharpness,G-sharpness,B-sharpness}
		true, // boolean absolute, // return absolutely calibrated data
		focusMeasurementParameters.lensDistanceWeightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives
		@@ -11129,18 +11217,25 @@ if (MORE_BUTTONS) {
		debugLevel
		);

		int ca=6;
		// int ca=6;
		String sZTxTy="";
		if (zTxTy!=null){
		sZTxTy="z="+IJ.d2s(zTxTy[0],3)+"um"+" tX="+IJ.d2s(zTxTy[1],3)+"um/mm"+" tY="+IJ.d2s(zTxTy[2],3)+"um/mm";
		}
		int [] actualPosition=focusingMotors.focusingHistory.getPosition();
		System.out.println("##"+focusingMotors.historySize()+": "+actualPosition[0]+", "+actualPosition[1]+", "+actualPosition[2]+
		": fDistance="+IJ.d2s(fDistance,3)+"um"+
		" Far/Near="+IJ.d2s(metrics[ca][0],3)+
		" Tilt X="+IJ.d2s(metrics[ca][1],3)+
		" Tilt Y="+IJ.d2s(metrics[ca][2],3)+
		": "+
		sZTxTy+
		" fDistanceOld="+IJ.d2s(fDistanceOld,3)+"um"+
		" Far/Near="+IJ.d2s(oldFarNear,3)+
		" Tilt X="+IJ.d2s(oldTx,3)+
		" Tilt Y="+IJ.d2s(oldTy,3)+
		" R50% average="+IJ.d2s(metrics[ca][3],3)+" sensor pixels,"+
		" A50% average="+IJ.d2s(metrics[ca][4],3)+" sensor pixels,"+
		" B50% average="+IJ.d2s(metrics[ca][5],3)+" sensor pixels,"+
		" R50%Center="+IJ.d2s(metrics[ca][6],3)+" sensor pixels"+
		" temp="+focusMeasurementParameters.sensorTemperature);
		double fDistance=(zTxTy==null)?fDistanceOld:zTxTy[0];
		if (debugLevel>1){
		String [] compColors={"green","red","blue","green","green","green","AVERAGE"};
		for (int c=0;c<metrics.length-1;c++) if (metrics[c]!=null){
		@@ -11162,7 +11257,6 @@ if (MORE_BUTTONS) {
		focusMeasurementParameters.result_B50=metrics[ca][5]; // last measured B50 (simailar, but R^4 are averaged)
		focusMeasurementParameters.result_RC50=metrics[ca][6]; // last measured RC50(R50 calculated only for the 2 center samples)
		}

		}

src/main/java/CalibrationHardwareInterface.java

+86 −20

Original line number	Diff line number	Diff line
		@@ -2977,7 +2977,25 @@ public class CalibrationHardwareInterface {
		fullResults
		);
		}

		public FocusingField.FocusingFieldMeasurement getThisFFMeasurement(
		FocusingField focusingField,
		String sTimestamp,
		double temperature,
		double[][] psfMetrics,
		double [][][][] fullResults){

		return focusingField.getFocusingFieldMeasurement(
		sTimestamp, //focusingState.getTimestamp(),
		temperature, //focusingState.getTemperature(),
		this.curpos, //focusingState.motorsPos,
		fullResults); //focusingState.getSamples());
		}



		/*
		* FocusingHistory.FocusingState focusingState
		public void addToHistory( String sTimestamp,double temperature, double[][] psfMetrics){ // null OK
		this.focusingHistory.add(
		sTimestamp,
		@@ -3004,6 +3022,7 @@ public class CalibrationHardwareInterface {
		}

		public void listHistory(
		boolean useLMA,
		String path,
		String lensSerial,
		String comment,
		@@ -3015,6 +3034,7 @@ public class CalibrationHardwareInterface {
		double weightY // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
		){
		listHistory(
		useLMA,
		path,
		"",
		lensSerial,
		@@ -3033,6 +3053,7 @@ public class CalibrationHardwareInterface {
		}

		public void listHistory(
		boolean useLMA,
		String path,
		String serialNumber,
		String lensSerial,
		@@ -3051,6 +3072,7 @@ public class CalibrationHardwareInterface {
		){

		this.focusingHistory.list(
		useLMA,
		path,
		serialNumber,
		lensSerial,
		@@ -3084,6 +3106,7 @@ public class CalibrationHardwareInterface {
		pY0,
		sampleCoord);
		}

		public FocusingField.FocusingFieldMeasurement getThisFFMeasurement(FocusingField focusingField){
		return getThisFFMeasurement(focusingField, -1);
		}
		@@ -3899,6 +3922,14 @@ public class CalibrationHardwareInterface {
		if ((index<0) \|\| (index>=this.history.size())) return null;
		return this.history.get(index).getCenterResolutions();
		}
		public double [] getzTxTy(int index){
		if ((index<0) \|\| (index>=this.history.size())) return null;
		return this.history.get(index).getzTxTy();
		}
		public double [] getzTxTy(){
		if (this.history.size()<1) return null;
		return getzTxTy(this.history.size()-1);
		}
		public int size(){
		return this.history.size();
		}
		@@ -5067,6 +5098,7 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		* @return array of 2 elements - {length at 0C, microns/degree}
		*/
		public double [] temperatureLinearApproximation(
		boolean useLMA,
		int numSamples, // number of last samples from history to use, 0 - use all
		double lensDistanceWeightK, // used in distance calculation
		double lensDistanceWeightY // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
		@@ -5079,8 +5111,11 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		int firstSample=this.history.size()-numSamples;

		for (int nSample=0;nSample<numSamples;nSample++){
		resolutions= this.history.get(firstSample+nSample).getCenterResolutions();
		data[nSample][0]=this.history.get(firstSample+nSample).getTemperature();
		if (useLMA){
		data[nSample][1]=this.history.get(firstSample+nSample).getzTxTy()[0];
		} else {
		resolutions= this.history.get(firstSample+nSample).getCenterResolutions();
		data[nSample][1]=getLensDistance(
		resolutions, // {R-sharpness,G-sharpness,B-sharpness}
		true, // boolean absolute, // return absolutely calibrated data
		@@ -5089,6 +5124,7 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		1 //debugLevel
		);
		}
		}
		PolynomialApproximation pa= new PolynomialApproximation(debugLevel);
		double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear
		return polyCoeff;
		@@ -5524,6 +5560,7 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		// todo - add "probe around" - 6/3 points, +/- for each direction (fraction of sigma?)

		public void list(
		boolean useLMA,
		String path,
		String lensSerial, // if null - do not add average
		String comment,
		@@ -5533,8 +5570,10 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		double weightRatioBlueToGreen,
		double weightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives
		double weightY){ // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
		list (path,
		"",
		list (
		useLMA,
		path,
		"", // serial; number
		lensSerial, // if null - do not add average
		comment,
		showIndividualComponents,
		@@ -5641,6 +5680,7 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "

		}
		public void list(
		boolean useLMA,
		String path,
		String serialNumber,
		String lensSerial, // if null - do not add average
		@@ -5701,15 +5741,22 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		if (showIndividualComponents) {
		for (int i=0;i<this.history.size();i++){
		FocusingState focusingState=this.history.get(i);
		double [] zTxTy=useLMA?focusingState.getzTxTy():null;
		double [][] metrics=focusingState.getMetrics(weightRatioRedToGreen,weightRatioBlueToGreen);
		double [][] resolution=focusingState.getSharpness(weightRatioRedToGreen,weightRatioBlueToGreen);
		double dist= getLensDistance(
		double dist= (zTxTy==null)?getLensDistance(
		focusingState.getCenterResolutions(), // {R-sharpness,G-sharpness,B-sharpness}
		true, //boolean absolute, // return absolutely calibrated data
		weightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives
		weightY, // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
		1); //int debugLevel
		1): //int debugLevel
		zTxTy[0];
		double [] averageMetrics=metrics[3];
		if (zTxTy!=null){
		averageMetrics=metrics[3].clone(); // to modify w/o changing original
		averageMetrics[1]=zTxTy[1]; // tiltX
		averageMetrics[2]=zTxTy[2]; // tiltY
		}
		double [] averageResolution=resolution[3];
		sb.append((i+1)+"\t");
		String timestamp=focusingState.getTimestamp();
		@@ -5779,9 +5826,15 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		for (int i=0;i<this.history.size();i++){
		// int parIndex=0;
		FocusingState focusingState=this.history.get(i);
		double [] zTxTy=useLMA?focusingState.getzTxTy():null;
		double [][] metrics=focusingState.getMetrics(weightRatioRedToGreen,weightRatioBlueToGreen);
		double [][] resolution=focusingState.getSharpness(weightRatioRedToGreen,weightRatioBlueToGreen);
		double [] averageMetrics=metrics[3];
		if (zTxTy!=null){
		averageMetrics=metrics[3].clone(); // to modify w/o changing original
		averageMetrics[1]=zTxTy[1]; // tiltX
		averageMetrics[2]=zTxTy[2]; // tiltY
		}
		double [] averageResolution=resolution[3];
		if (!justSummary) sb.append((i+1)+"\t");
		String timestamp=focusingState.getTimestamp();
		@@ -5806,12 +5859,13 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		sums[4]+=focusingState.motorsPos[0];
		sums[5]+=focusingState.motorsPos[1];
		sums[6]+=focusingState.motorsPos[2];
		double dist= getLensDistance(
		double dist= (zTxTy==null)?getLensDistance(
		focusingState.getCenterResolutions(), // {R-sharpness,G-sharpness,B-sharpness}
		true, //boolean absolute, // return absolutely calibrated data
		weightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives
		weightY, // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
		1); //int debugLevel
		1): //int debugLevel
		zTxTy[0];
		if (Double.isNaN(dist)){
		if (!justSummary) sb.append("\t---");
		} else {
		@@ -6199,7 +6253,19 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
		1.0,
		weightRatioBlueToGreen);
		}
		// alternative mode (from aberration model) ising metrics[6][]
		public double [] getzTxTy(){
		if (this.psfMetricses==null){
		return null;
		}
		if ((this.psfMetricses.length<7) \|\| (this.psfMetricses[6]==null)) {
		System.out.println("BUG? psfMetrics does not have line 6 with lens berration model z, tx, ty");
		return null;
		}
		double [] zTxTy={this.psfMetricses[6][0],this.psfMetricses[6][1],this.psfMetricses[6][2]};
		return zTxTy;

		}
		public double [][] getMetrics(
		double weightRed,
		double weightGreen,

src/main/java/FocusingField.java

+73 −56

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/LensAdjustment.java

+12 −1

Original line number	Diff line number	Diff line
		@@ -195,6 +195,7 @@ public class LensAdjustment {
		public String gridGeometryFile="";
		public String initialCalibrationFile="";
		public String focusingHistoryFile="";
		public boolean useLMAMetrics=true; // measure/report focal distance and tilts using lens model/LMA (when available)
		public String strategyFile="";
		public String resultsSuperDirectory=""; // directory with subdirectories named as serial numbers to stro results
		public int EEPROM_channel=1; // EEPROM channel to read serial number from
		@@ -430,6 +431,7 @@ public class LensAdjustment {
		String strategyFile,
		String resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results
		String focusingHistoryFile,
		boolean useLMAMetrics, // measure/report focal distance and tilts using lens model/LMA (when available)
		int EEPROM_channel, // EEPROM channel to read serial number from
		boolean saveResults, // save focusing results
		boolean showResults, // show focusing (includingh intermediate) results
		@@ -577,6 +579,7 @@ public class LensAdjustment {
		this.strategyFile=strategyFile;
		this.resultsSuperDirectory=resultsSuperDirectory; // directory with subdirectories named as serial numbers to stro results
		this.focusingHistoryFile=focusingHistoryFile;
		this.useLMAMetrics=useLMAMetrics; // measure/report focal distance and tilts using lens model/LMA (when available)
		this.EEPROM_channel=EEPROM_channel; // EEPROM channel to read serial number from
		this.saveResults=saveResults; // save focusing results
		this.showResults=showResults; // show focusing (includingh intermediate) results
		@@ -725,6 +728,7 @@ public class LensAdjustment {
		this.strategyFile,
		this.resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results
		this.focusingHistoryFile,
		this.useLMAMetrics, // measure/report focal distance and tilts using lens model/LMA (when available)
		this.EEPROM_channel,// EEPROM channel to read serial number from
		this.saveResults, // save focusing results
		this.showResults, // show focusing (includingh intermediate) results
		@@ -871,6 +875,7 @@ public class LensAdjustment {
		properties.setProperty(prefix+"strategyFile",this.strategyFile+"");
		properties.setProperty(prefix+"resultsSuperDirectory",this.resultsSuperDirectory+"");
		properties.setProperty(prefix+"focusingHistoryFile",this.focusingHistoryFile+"");
		properties.setProperty(prefix+"useLMAMetrics",this.useLMAMetrics+"");
		properties.setProperty(prefix+"serialNumber",this.serialNumber+"");
		if (!Double.isNaN(this.sensorTemperature))properties.setProperty(prefix+"sensorTemperature",this.sensorTemperature+"");
		if (!Double.isNaN(this.result_lastKT))properties.setProperty(prefix+"result_lastKT",this.result_lastKT+"");
		@@ -1030,6 +1035,9 @@ public class LensAdjustment {
		if (properties.getProperty(prefix+"focusingHistoryFile")!=null)
		this.focusingHistoryFile=properties.getProperty(prefix+"focusingHistoryFile");

		if (properties.getProperty(prefix+"useLMAMetrics")!=null)
		this.useLMAMetrics=Boolean.parseBoolean(properties.getProperty(prefix+"useLMAMetrics"));

		if (properties.getProperty(prefix+"serialNumber")!=null)
		this.serialNumber=properties.getProperty(prefix+"serialNumber");
		// this.serialNumber is only written, but never read from the configuration file (only from devivce)
		@@ -1441,7 +1449,8 @@ public class LensAdjustment {
		gd.addStringField ("Initial camera intrinsic/extrinsic parametres file", this.initialCalibrationFile,40);
		gd.addStringField ("Levenberg-Marquardt algorithm strategy file", this.strategyFile,40);
		gd.addStringField ("Focusing results superdirectory (individual will be named by serial numbers)", this.resultsSuperDirectory,40);
		gd.addStringField ("Measurement history (acquired during \"Scan Calib LMA\" file", this.focusingHistoryFile,80);
		gd.addStringField ("Measurement history (acquired during \"Scan Calib LMA\") file", this.focusingHistoryFile,80);
		gd.addCheckbox ("Use lens aberration model (if available) for focal distance and tilts", this.useLMAMetrics);
		gd.addNumericField("EEPROM channel to read sensor serial number from", this.EEPROM_channel, 0,4,"");
		gd.addCheckbox ("Save SFE focusing results (including intermediate) ", this.saveResults);
		gd.addCheckbox ("Show SFE focusing results (including intermediate) ", this.showResults);
		@@ -1618,6 +1627,8 @@ public class LensAdjustment {
		this.strategyFile= gd.getNextString();
		this.resultsSuperDirectory= gd.getNextString();
		this.focusingHistoryFile= gd.getNextString();
		this.useLMAMetrics = gd.getNextBoolean();

		this.EEPROM_channel= (int) gd.getNextNumber();
		this.saveResults= gd.getNextBoolean();
		this.showResults= gd.getNextBoolean();

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