Adding LMA version to averaging/temperature scan commands (b75d6c0f) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+98 −2

Original line number	Original line	Diff line number	Diff line
	@@ -50,6 +50,7 @@ import java.util.regex.Pattern;




	//import FocusingField.FocusingFieldMeasurement;		//import FocusingField.FocusingFieldMeasurement;
	//import FocusingField.MeasuredSample;		//import FocusingField.MeasuredSample;
	import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/		import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/
	@@ -5018,6 +5019,8 @@ if (MORE_BUTTONS) {
	if (label.equals("Temp. Scan") \|\| label.equals("Focus Average")) {		if (label.equals("Temp. Scan") \|\| label.equals("Focus Average")) {
	checkSerialAndRestore(); // returns true if did not change or was restored		checkSerialAndRestore(); // returns true if did not change or was restored
	boolean modeAverage=label.equals("Focus Average");		boolean modeAverage=label.equals("Focus Average");
			boolean noTiltScan=true;
			boolean useLMA=true;
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
	FOCUS_MEASUREMENT_PARAMETERS,		FOCUS_MEASUREMENT_PARAMETERS,
	@@ -5033,6 +5036,8 @@ if (MORE_BUTTONS) {
	gd.addCheckbox("Turn lasers off to protect from overheating",true);		gd.addCheckbox("Turn lasers off to protect from overheating",true);
	}		}
	gd.addCheckbox("Erase previous measurement history",modeAverage);		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);
	double scanMinutes=modeAverage?1.0:30.0;		double scanMinutes=modeAverage?1.0:30.0;
	gd.addNumericField("Measure for ", scanMinutes , 1,5," minutes");		gd.addNumericField("Measure for ", scanMinutes , 1,5," minutes");
	gd.showDialog();		gd.showDialog();
	@@ -5043,6 +5048,9 @@ if (MORE_BUTTONS) {
	if (MASTER_DEBUG_LEVEL>0) System.out.println ("Turned laser pointers off to protect from overheating");		if (MASTER_DEBUG_LEVEL>0) System.out.println ("Turned laser pointers off to protect from overheating");
	}		}
	if (gd.getNextBoolean()) MOTORS.clearHistory();		if (gd.getNextBoolean()) MOTORS.clearHistory();
			noTiltScan=!gd.getNextBoolean();
			useLMA=gd.getNextBoolean();
			// int startHistPos=MOTORS.historySize();
	scanMinutes=gd.getNextNumber();		scanMinutes=gd.getNextNumber();
	long startTime=System.nanoTime();		long startTime=System.nanoTime();
	long endTime=startTime+(long) (6E10*scanMinutes);		long endTime=startTime+(long) (6E10*scanMinutes);
	@@ -5079,7 +5087,45 @@ if (MORE_BUTTONS) {
	}		}

	}		}
			// LMA version

			double pX0=FOCUS_MEASUREMENT_PARAMETERS.result_PX0;
			double pY0=FOCUS_MEASUREMENT_PARAMETERS.result_PY0;
			double [][][] sampleCoord=FOCUS_MEASUREMENT_PARAMETERS.sampleCoordinates( //{x,y,r}
			pX0, // lens center on the sensor
			pY0);
			if (useLMA){
			FOCUSING_FIELD= new FocusingField(
			FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
			FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
			FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
			pX0,
			pY0,
			sampleCoord,
			this.SYNC_COMMAND.stopRequested);
			FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
			FOCUSING_FIELD.setAdjustMode(false);
			if (PROPERTIES!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", PROPERTIES);
			MOTORS.addCurrentHistoryToFocusingField(
			FOCUSING_FIELD,
			(runs==0)?0:(MOTORS.historySize()-runs),
			MOTORS.historySize()); // all newly acquired
			if (modeAverage){ // calculate/show average over the last run - only in "average" mode
			double [] ZTM=FOCUSING_FIELD.averageZTM(noTiltScan); // no tilt scan - faster
			if (MASTER_DEBUG_LEVEL>0) {
			String msg="Failed to calulate average focus/tilt";
			if (ZTM!=null) msg="Average:\n"+
			"Relative focal shift "+IJ.d2s(ZTM[0],3)+"um\n"+
			"Horizontal tilt "+IJ.d2s(ZTM[1],3)+"um/mm\n"+
			"Vertical tilt "+IJ.d2s(ZTM[2],3)+"um/mm\n"+
			"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) {		if (FOCUS_MEASUREMENT_PARAMETERS.saveResults) {
	String dir=getResultsPath(FOCUS_MEASUREMENT_PARAMETERS);		String dir=getResultsPath(FOCUS_MEASUREMENT_PARAMETERS);
	File dFile=new File(dir);		File dFile=new File(dir);
	@@ -5113,8 +5159,16 @@ if (MORE_BUTTONS) {
	FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,		FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,
	FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT		FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT
	);		);
			if (useLMA){
			String focusingPath=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+".history-xml";
			System.out.println("Saving measurement history to "+focusingPath);
			FOCUSING_FIELD.saveXML(focusingPath);
	}		}
			}
			// Calculate and showaverage distances and tilts for measured history

	if (!modeAverage) {		if (!modeAverage) {

	double [] lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(		double [] lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
	runs, // number of last samples from history to use, 0 - use all		runs, // number of last samples from history to use, 0 - use all
	FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightK,		FOCUS_MEASUREMENT_PARAMETERS.lensDistanceWeightK,
	@@ -5140,6 +5194,48 @@ if (MORE_BUTTONS) {
	System.out.println(msg);		System.out.println(msg);
	IJ.showMessage("Info",msg);		IJ.showMessage("Info",msg);
	}		}
			// Now in LMA mode - recalculate and overwrite
			if (useLMA){
			FOCUSING_FIELD= new FocusingField(
			FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
			FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
			FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
			pX0,
			pY0,
			sampleCoord,
			this.SYNC_COMMAND.stopRequested);
			FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
			FOCUSING_FIELD.setAdjustMode(false);
			if (PROPERTIES!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", PROPERTIES);
			MOTORS.addCurrentHistoryToFocusingField(FOCUSING_FIELD); // all, not just newly acquired
			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); // no tilt scan (supposed to be adjusted
			lastKT=MOTORS.focusingHistory.temperatureLinearApproximation(
			allZTM,
			runs
			);
			allKT=MOTORS.focusingHistory.temperatureLinearApproximation(
			allZTM,
			0
			);
			FOCUS_MEASUREMENT_PARAMETERS.result_lastKT=lastKT[1]; // focal distance temperature coefficient (um/C), measured from last run
			FOCUS_MEASUREMENT_PARAMETERS.result_lastFD20=lastKT[0]+20*lastKT[1]; // focal distance for 20C, measured from last run
			FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT=allKT[1]; // focal distance temperature coefficient (um/C), measured from all the measurement histgory
			FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryFD20=allKT[0]+20*allKT[1]; // focal distance for 20C, measured from all the measurement histgory
			if (MASTER_DEBUG_LEVEL>0){
			String msg=
			"Determined by LMA: Focal distance temperature expansion is "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastKT,2)+
			" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryKT,2)+")"+
			" microns per C, measured from this run (measured from all the history)\n"+
			"Focal distance at 20C is "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_lastFD20,2)+
			" ("+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.result_allHistoryFD20,2)+")"+
			" microns, measured from this run (measured from all the history)";
			System.out.println(msg);
			IJ.showMessage("Info",msg);
			}
			}
	}		}
	saveCurrentConfig();		saveCurrentConfig();
	return;		return;
	@@ -8738,7 +8834,7 @@ if (MORE_BUTTONS) {
	//get measurement		//get measurement
	FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);		FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);
	// calculate z, tx, ty, m1,m2,m3		// calculate z, tx, ty, m1,m2,m3
	double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(fFMeasurement,false);		double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(false,fFMeasurement,false); // allow tilt scan
	// show dialog: Apply, re-calculate, exit		// show dialog: Apply, re-calculate, exit
	int [] currentMotors=fFMeasurement.motors;		int [] currentMotors=fFMeasurement.motors;
	int [] newMotors=currentMotors.clone();		int [] newMotors=currentMotors.clone();
	@@ -8836,7 +8932,7 @@ if (MORE_BUTTONS) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);		FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
	if (parallelMove){ // ignore/recalculate newMotors data		if (parallelMove){ // ignore/recalculate newMotors data
	zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(fFMeasurement,true); // recalculate with parallel move only		zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(false,fFMeasurement,true); // recalculate with parallel move only, allow tilt scan
	newMotors=currentMotors.clone();		newMotors=currentMotors.clone();
	if (zTxTyM1M2M3!=null){		if (zTxTyM1M2M3!=null){
	newMotors[0]=(int) Math.round(zTxTyM1M2M3[3]);		newMotors[0]=(int) Math.round(zTxTyM1M2M3[3]);

src/main/java/CalibrationHardwareInterface.java

+39 −7

Original line number	Original line	Diff line number	Diff line
	@@ -3100,14 +3100,21 @@ public class CalibrationHardwareInterface {
	return null;		return null;
	}		}

	// public void addCurrentHistoryToFocusingField(FocusingField focusingField){		public void addCurrentHistoryToFocusingField(
	// this.focusingHistory.addCurrentHistory(focusingField);		FocusingField focusingField,
	// }		int start,
	public void addCurrentHistoryToFocusingField(FocusingField focusingField){		int end){
	for (int i=0;i<historySize();i++){		for (int i=start;i<end;i++){
	addCurrentHistoryToFocusingField(focusingField,i);		addCurrentHistoryToFocusingField(focusingField,i);
	}		}
	// this.focusingHistory.addCurrentHistory(focusingField);		}

			public void addCurrentHistoryToFocusingField(FocusingField focusingField){
			addCurrentHistoryToFocusingField(
			focusingField,
			0,
			historySize()
			);
	}		}

	public void addCurrentHistoryToFocusingField(		public void addCurrentHistoryToFocusingField(
	@@ -5086,6 +5093,31 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
	double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear		double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear
	return polyCoeff;		return polyCoeff;
	}		}

			public double [] temperatureLinearApproximation(
			double [][] ZTM, // Z, tXx, tY, m1,m2,m3 found with LMA
			int numSamples // number of last samples from history to use, 0 - use all
			){
			if (numSamples<=0) numSamples=this.history.size();
			if (numSamples>this.history.size()) numSamples=this.history.size();
			int firstSample=this.history.size()-numSamples;

			int numGoodSamples=0;
			for (int nSample=0;nSample<numSamples;nSample++){
			if (ZTM[firstSample+nSample]!=null) numGoodSamples++;
			}
			double [][] data =new double [numGoodSamples][2]; // no weights
			int index=0;
			for (int nSample=0;nSample<numSamples;nSample++) if (ZTM[firstSample+nSample]!=null) {
			data[index][0]=this.history.get(firstSample+nSample).getTemperature();
			data[index++][1]=ZTM[firstSample+nSample][0]; // Z
			}
			PolynomialApproximation pa= new PolynomialApproximation(debugLevel);
			double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear
			return polyCoeff;
			}


	/**		/**
	* will return same coordinates if tolerances are met		* will return same coordinates if tolerances are met
	* @param useTheBest		* @param useTheBest

src/main/java/FocusingField.java

+26 −2

Original line number	Original line	Diff line number	Diff line
	@@ -4373,7 +4373,31 @@ public boolean LevenbergMarquardt(
	}		}

	//,		//,
			public double [][] getAllZTM(
			boolean noTiltScan){
			double [][] result =new double[measurements.size()][6];
			for (int i=0;i<result.length;i++) result[i]=adjustLMA(noTiltScan,measurements.get(i),false);
			return result;
			}

			public double [] averageZTM(
			boolean noTiltScan){
			double [] result =new double[6];
			for (int i=0;i<result.length;i++) result[i]=0.0;
			int num=0;
			for (FocusingFieldMeasurement measurement:measurements){
			double [] ZTM = adjustLMA(noTiltScan,measurement,false);
			if (ZTM!=null) {
			for (int i=0;i<result.length;i++) result[i]+=ZTM[i];
			num++;
			}
			}
			if (num==0) return null;
			for (int i=0;i<result.length;i++) result[i]/=num;
			return result;
			}
	public double [] adjustLMA (		public double [] adjustLMA (
			boolean noTiltScan,
	FocusingFieldMeasurement measurement,		FocusingFieldMeasurement measurement,
	boolean parallelMove){		boolean parallelMove){
	if (!testMeasurement(		if (!testMeasurement(
	@@ -4381,8 +4405,8 @@ public boolean LevenbergMarquardt(
	zMin, //+best_qb_corr[0],		zMin, //+best_qb_corr[0],
	zMax, //+best_qb_corr[0],		zMax, //+best_qb_corr[0],
	zStep,		zStep,
	tMin,		(noTiltScan?0.0:tMin),
	tMax,		(noTiltScan?0.0:tMax),
	tStep)) {		tStep)) {
	if (debugLevel>0) System.out.println("adjustLMA() failed");		if (debugLevel>0) System.out.println("adjustLMA() failed");
	return null;		return null;

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