removed obsolete data output (1a664c2b) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+129 −92

Original line number	Diff line number	Diff line
		@@ -829,6 +829,7 @@ if (MORE_BUTTONS) {
		addButton("Test measurement", panelCurvature,color_debug);
		addButton("Optimize qualB", panelCurvature,color_debug);
		addButton("Focus/Tilt LMA", panelCurvature,color_process);
		addButton("Post-UV Adjust", panelCurvature,color_process);
		add(panelCurvature);

		//panelGoniometer
		@@ -4372,11 +4373,12 @@ if (MORE_BUTTONS) {
		// int [] mmm= MOTORS.focusingHistory.getPosition();

		//System.out.println("@@"+MOTORS.historySize()+": "+MOTORS.curpos[0]+", "+MOTORS.curpos[1]+", "+MOTORS.curpos[2]+" --- "+mmm[0]+", "+mmm[1]+", "+mmm[2]);

		if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy){
		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distamnce from center PSF
		FOCUS_MEASUREMENT_PARAMETERS,
		MOTORS.getMicronsPerStep(), //double micronsPerStep,
		DEBUG_LEVEL);
		}
		//System.out.println("@@@"+MOTORS.historySize()+": "+MOTORS.curpos[0]+", "+MOTORS.curpos[1]+", "+MOTORS.curpos[2]+" --- "+mmm[0]+", "+mmm[1]+", "+mmm[2]);
		boolean autoMove= label.equals("Auto Focus/Tilt");
		boolean fineFocus=label.equals("Fine Focus");
		@@ -4934,11 +4936,9 @@ if (MORE_BUTTONS) {
		FOCUSING_FIELD.testQualB(true); // public double[] testQualB(boolean interactive)
		return;
		}



		/* ======================================================================== */
		if (label.equals("Focus/Tilt LMA")) {
		if (label.equals("Focus/Tilt LMA") \|\| label.equals("Post-UV Adjust")) {
		int adjustMode=label.equals("Focus/Tilt LMA")?0:1;
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		if (FOCUSING_FIELD==null) {
		if (DEBUG_LEVEL>0) System.out.println("FOCUSING_FIELD==null, trying to restore from the previously saved file");
		@@ -4959,12 +4959,13 @@ if (MORE_BUTTONS) {
		}
		}
		// Just for old focal distance calculation
		if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy){
		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
		FOCUS_MEASUREMENT_PARAMETERS,
		MOTORS.getMicronsPerStep(), //double micronsPerStep,
		DEBUG_LEVEL);

		while (adjustFocusTiltLMA());
		}
		while (adjustFocusTiltLMA(adjustMode));
		return;
		}
		//
		@@ -5426,11 +5427,12 @@ if (MORE_BUTTONS) {
		FOCUS_MEASUREMENT_PARAMETERS.result_PX0,
		FOCUS_MEASUREMENT_PARAMETERS.result_PY0);
		}

		if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy){
		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
		FOCUS_MEASUREMENT_PARAMETERS,
		MOTORS.getMicronsPerStep(), //double micronsPerStep,
		DEBUG_LEVEL);
		}
		moveAndMaybeProbe(
		true, // just move, not probe
		null, // no move, just measure
		@@ -5500,10 +5502,12 @@ if (MORE_BUTTONS) {
		String [] zTxTyNames={"z", "tx","ty"};
		// boolean useLMA=true;
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy){
		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
		FOCUS_MEASUREMENT_PARAMETERS,
		MOTORS.getMicronsPerStep(), //double micronsPerStep,
		DEBUG_LEVEL);
		}
		GenericDialog gd = new GenericDialog(modeAverage?"Averaging measurements":"Temperature Scan");
		//replayMode
		double scanMinutes=modeAverage?2.0:30.0;
		@@ -5938,7 +5942,7 @@ if (MORE_BUTTONS) {
		"Average Tilt y: "+IJ.d2s(zcZ0TxTy[0][2],3)+"um/mm\n";
		System.out.println(msg);
		gd.addMessage(msg);
		gd.addCheckbox("Store calculated tilts, defaultValue",FOCUSING_FIELD.updateAverageTilts);
		gd.addCheckbox("Store calculated tilts",FOCUSING_FIELD.updateAverageTilts);
		}
		gd.showDialog();
		if (!gd.wasCanceled()){
		@@ -9918,7 +9922,11 @@ if (MORE_BUTTONS) {
		}


		public boolean adjustFocusTiltLMA(){
		/**
		* @param adjustMode - 0 normal, using motors. 1 - post-UV manual adjustment
		* @return
		*/
		public boolean adjustFocusTiltLMA(int adjustMode){
		// just for reporting distance old way
		/*
		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
		@@ -9940,8 +9948,11 @@ if (MORE_BUTTONS) {
		FOCUS_MEASUREMENT_PARAMETERS.result_PX0,
		FOCUS_MEASUREMENT_PARAMETERS.result_PY0);
		}
		int [] adjustModeAllCommon={1,1,1};
		// save zTxTyAdjustMode used in moveMeasureAndSave, and overwrite it with adjustModeAllCommon (so new tX,tY will be calculated each time)
		int [] savedZTxTyAdjustMode=FOCUSING_FIELD.zTxTyAdjustMode.clone();
		FOCUSING_FIELD.zTxTyAdjustMode=adjustModeAllCommon.clone();
		// No-move measure, add to history

		moveAndMaybeProbe(
		true, // just move, not probe
		null, // no move, just measure
		@@ -9961,16 +9972,17 @@ if (MORE_BUTTONS) {
		UPDATE_STATUS,
		MASTER_DEBUG_LEVEL,
		DISTORTION.loop_debug_level);
		// restore configured FOCUSING_FIELD.zTxTyAdjustMode
		FOCUSING_FIELD.zTxTyAdjustMode=savedZTxTyAdjustMode.clone();
		//get measurement
		FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);
		// calculate z, tx, ty, m1,m2,m3
		int [] adjustModeAllCommon={1,1,1};
		double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(
		adjustModeAllCommon, // FOCUSING_FIELD.zTxTyAdjustMode,
		false, // allow tilt scan
		fFMeasurement,
		false, // parallel move
		true, // boolean noQualB, // do not re-claculate testQualB
		true, // boolean noQualB, // do not re-calculate testQualB
		false); // boolean noAdjust); // do not calculate correction
		// show dialog: Apply, re-calculate, exit
		int [] currentMotors=fFMeasurement.motors;
		@@ -10012,6 +10024,7 @@ if (MORE_BUTTONS) {
		System.out.println("Relative to optimal focal shift "+IJ.d2s(zTxTy[0],3)+" um ("+IJ.d2s(FOCUSING_FIELD.targetRelFocalShift,3)+"um)");
		System.out.println("Relative to optimal horizontal tilt "+IJ.d2s(zTxTy[1],3)+" um/mm ("+IJ.d2s(FOCUSING_FIELD.targetRelTiltX,3)+"um/mm)");
		System.out.println("Relative to optimal vertical tilt "+IJ.d2s(zTxTy[2],3)+" um/mm ("+IJ.d2s(FOCUSING_FIELD.targetRelTiltY,3)+"um/mm)");
		if (adjustMode==0) {
		for (int i=0;i<newMotors.length;i++){
		System.out.println("Suggested for motor "+(i+1)+" "+newMotors[i]+" ("+currentMotors[i]+")");
		}
		@@ -10022,6 +10035,7 @@ if (MORE_BUTTONS) {
		else System.out.println("Suggested rotation for screw # "+(i+1)+
		" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
		}
		} else if (adjustMode==1) {
		if (postUVScrews!=null) {
		System.out.println("----- Post-UV fixture screw adjustments -----");
		for (int i=0;i<postUVScrews.length;i++){
		@@ -10032,6 +10046,7 @@ if (MORE_BUTTONS) {
		" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
		}
		}
		}
		System.out.println("----- end of Focus/tilt measurement results -----");

		if (MASTER_DEBUG_LEVEL>0) System.out.println(FOCUSING_FIELD.showSamples());
		@@ -10053,7 +10068,7 @@ if (MORE_BUTTONS) {
		gd.addCheckbox("Optimize tiltX", (FOCUSING_FIELD.qualBOptimizeMode & 2) != 0);
		gd.addCheckbox("Optimize tiltY", (FOCUSING_FIELD.qualBOptimizeMode & 4) != 0);


		if (adjustMode==0) {
		gd.addNumericField("Motor 1",newMotors[0],0,5,"steps ("+currentMotors[0]+")");
		gd.addNumericField("Motor 2",newMotors[1],0,5,"steps ("+currentMotors[1]+")");
		gd.addNumericField("Motor 3",newMotors[2],0,5,"steps ("+currentMotors[2]+")");
		@@ -10063,6 +10078,8 @@ if (MORE_BUTTONS) {
		if (manualScrewsCW[i]>=0) gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)");
		else gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
		}
		} else if (adjustMode==1) {

		if (postUVScrews!=null) {
		gd.addMessage("Suggested rotation of the post-UV fixture screws (far left, near left, right) ---");
		for (int i=0;i<postUVScrews.length;i++){
		@@ -10075,6 +10092,7 @@ if (MORE_BUTTONS) {
		gd.addNumericField("Screw "+i+" sensitivity", FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity[i], 4,6,"um/turn CW");
		}
		}
		}
		gd.addNumericField("Scale movement",scaleMovement,3,5,"x");
		gd.addCheckbox("Recalculate and apply parallel move only",parallelMove); // should be false after manual movement

		@@ -10089,11 +10107,13 @@ if (MORE_BUTTONS) {
		gd.addNumericField("Tilt min",FOCUSING_FIELD.tMin,2,5,"um/mm");
		gd.addNumericField("Tilt max",FOCUSING_FIELD.tMax,2,5,"um/mm");
		gd.addNumericField("Tilt step",FOCUSING_FIELD.tStep,2,5,"um/mm");
		gd.addCheckbox("Store calculated tilts",FOCUSING_FIELD.updateAverageTilts);
		gd.addCheckbox("Show current PSF",showPSF);

		if (adjustMode==0) {
		gd.addNumericField("Motor anti-hysteresis travel (last measured was "+IJ.d2s(FOCUS_MEASUREMENT_PARAMETERS.measuredHysteresis,0)+")", FOCUS_MEASUREMENT_PARAMETERS.motorHysteresis, 0,7,"motors steps");
		}
		gd.addNumericField("Debug Level:", MASTER_DEBUG_LEVEL, 0);
		gd.enableYesNoCancel("Apply movement","Re-measure"); // default OK (on enter) - "Apply"
		if (adjustMode==0) gd.enableYesNoCancel("Apply movement","Re-measure"); // default OK (on enter) - "Apply"
		WindowTools.addScrollBars(gd);
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		@@ -10105,16 +10125,17 @@ if (MORE_BUTTONS) {
		FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?1:0;
		FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?2:0;
		FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?4:0;

		if (adjustMode==0) {
		newMotors[0]= (int) gd.getNextNumber();
		newMotors[1]= (int) gd.getNextNumber();
		newMotors[2]= (int) gd.getNextNumber();

		} else if (adjustMode==1) {
		if (postUVScrews!=null) {
		for (int i=0;i<FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity.length;i++){
		FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity[i]=gd.getNextNumber();
		}
		}
		}
		scaleMovement= gd.getNextNumber();
		parallelMove= gd.getNextBoolean();
		FOCUSING_FIELD.filterZ= gd.getNextBoolean();
		@@ -10128,11 +10149,27 @@ if (MORE_BUTTONS) {
		FOCUSING_FIELD.tMin= gd.getNextNumber();
		FOCUSING_FIELD.tMax= gd.getNextNumber();
		FOCUSING_FIELD.tStep= gd.getNextNumber();
		FOCUSING_FIELD.updateAverageTilts= gd.getNextBoolean();

		showPSF= gd.getNextBoolean();
		if (adjustMode==0) {
		FOCUS_MEASUREMENT_PARAMETERS.motorHysteresis= (int) gd.getNextNumber();
		}
		MASTER_DEBUG_LEVEL=( int) gd.getNextNumber();
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
		if (FOCUSING_FIELD.updateAverageTilts){
		double[][]zTxTyAbsRel=FOCUSING_FIELD.getZ0TxTyAbsRel(); // z - z0, not zc here !
		if (zTxTyAbsRel!=null){
		FOCUSING_FIELD.avgTx= zTxTyAbsRel[0][1]; // average absolute tilt X (optionally used when finding Z of the glued SFE)
		FOCUSING_FIELD.avgTy= zTxTyAbsRel[0][2]; // average absolute tilt Y (optionally used when finding Z of the glued SFE)
		FOCUS_MEASUREMENT_PARAMETERS.result_fDistance=zTxTy[0];
		FOCUS_MEASUREMENT_PARAMETERS.result_tiltX= zTxTy[1];
		FOCUS_MEASUREMENT_PARAMETERS.result_tiltY= zTxTy[2];
		}
		}


		if (showPSF){
		if (PSF_KERNEL_MAP==null){
		IJ.showMessage("Warning","PSF_KERNEL_MAP is null, nothing to show" );
		@@ -10156,6 +10193,7 @@ if (MORE_BUTTONS) {
		}
		}
		}

		if (parallelMove){ // ignore/recalculate newMotors data
		int [] adjustZOnly={1,0,0};
		zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(
		@@ -10182,7 +10220,7 @@ if (MORE_BUTTONS) {
		newMotors[1]=currentMotors[1]+((int) Math.round((newMotors[1]-currentMotors[1])*scaleMovement));
		newMotors[2]=currentMotors[2]+((int) Math.round((newMotors[2]-currentMotors[2])*scaleMovement));

		if (gd.wasOKed()){
		if ((adjustMode==0) && gd.wasOKed()){
		// Move, no measure
		MOTORS.moveElphel10364Motors(
		true, //boolean wait,
		@@ -12046,14 +12084,16 @@ 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 fDistanceOld=focusingMotors.focusingHistory.getLensDistance(
		double fDistanceOld=Double.NaN;
		if (FOCUS_MEASUREMENT_PARAMETERS.showLegacy) {
		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
		focusMeasurementParameters.lensDistanceWeightY, // R-frac, B-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
		debugLevel
		);

		}
		// int ca=6;
		String sZTxTy="";
		if (zTxTy!=null){
		@@ -12063,8 +12103,7 @@ if (MORE_BUTTONS) {
		System.out.println("##"+focusingMotors.historySize()+": "+actualPosition[0]+", "+actualPosition[1]+", "+actualPosition[2]+
		": "+
		sZTxTy+
		" fDistanceOld="+IJ.d2s(fDistanceOld,3)+"um"+
		" Far/Near="+IJ.d2s(oldFarNear,3)+
		(FOCUS_MEASUREMENT_PARAMETERS.showLegacy?(" 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,"+
		@@ -12096,8 +12135,6 @@ if (MORE_BUTTONS) {
		}
		}



		public boolean moveAndMeasureSharpness(
		int [] newMotorPos, // null OK
		CalibrationHardwareInterface.FocusingMotors focusingMotors,

src/main/java/LensAdjustment.java

+12 −5

Original line number	Diff line number	Diff line
		@@ -233,7 +233,7 @@ public class LensAdjustment {
		public String lensSerial=""; // Lens serial number
		public boolean askLensSerial=true; // Ask lens serial on camera power cycle
		public double reportTemperature=50; // temperature to report focal length

		public boolean showLegacy=false; // Show old focusing parameters (most are not supported anyway)
		public boolean includeLensSerial=true; // add lens serial to config filename
		public double centerDeltaX=0.0; // required X-difference between lens center and sensor center
		public double centerDeltaY=0.0; // required Y-difference between lens center and sensor center
		@@ -606,7 +606,8 @@ public class LensAdjustment {
		boolean cameraIsConfigured,
		int [] motorPos,
		double [] ampsSeconds, // cumulative Amps*seconds (read only, but will be saved/restored)
		double reportTemperature // temperature to report focal length
		double reportTemperature, // temperature to report focal length
		boolean showLegacy
		){
		this.gridGeometryFile=gridGeometryFile;
		this.initialCalibrationFile=initialCalibrationFile;
		@@ -763,7 +764,7 @@ public class LensAdjustment {
		this.motorPos=motorPos;
		this.ampsSeconds=ampsSeconds; // cumulative Amps*seconds (read only, but will be saved/restored)
		this.reportTemperature=reportTemperature;

		this.showLegacy=showLegacy;
		}
		public FocusMeasurementParameters clone(){
		return new FocusMeasurementParameters(
		@@ -921,7 +922,8 @@ public class LensAdjustment {
		this.cameraIsConfigured,
		this.motorPos,
		this.ampsSeconds, // cumulative Amps*seconds (read only, but will be saved/restored)
		this.reportTemperature
		this.reportTemperature,
		this.showLegacy
		);
		}
		public void setProperties(String prefix,Properties properties){
		@@ -1092,6 +1094,7 @@ public class LensAdjustment {
		for (int i=0;i<this.ampsSeconds.length;i++)
		properties.setProperty(prefix+"ampsSeconds_"+i,this.ampsSeconds[i]+"");
		properties.setProperty(prefix+"reportTemperature",this.reportTemperature+"");
		properties.setProperty(prefix+"showLegacy",this.showLegacy+"");
		}
		public void getProperties(String prefix,Properties properties){
		if (properties.getProperty(prefix+"gridGeometryFile")!=null)
		@@ -1427,6 +1430,8 @@ public class LensAdjustment {
		this.ampsSeconds[i]=Double.parseDouble(properties.getProperty(prefix+"ampsSeconds_"+i));
		if (properties.getProperty(prefix+"reportTemperature")!=null)
		this.reportTemperature=Double.parseDouble(properties.getProperty(prefix+"reportTemperature"));
		if (properties.getProperty(prefix+"showLegacy")!=null)
		this.showLegacy=Boolean.parseBoolean(properties.getProperty(prefix+"showLegacy"));
		}
		public boolean getLensSerial(){
		while (true) { // loop until OK-ed
		@@ -1696,6 +1701,7 @@ public class LensAdjustment {

		gd.addMessage("-----");
		gd.addNumericField("Report focal length at this temperature", this.reportTemperature, 1,5,"C");
		gd.addCheckbox ("Show legacy focusing parameters (most are already not supported anyway)", this.showLegacy);

		if (!Double.isNaN(this.sensorTemperature)) gd.addMessage("Last measured sensor temperature is "+this.sensorTemperature+" C");

		@@ -1888,6 +1894,7 @@ public class LensAdjustment {
		this.postUVscrewSensitivity[i]= gd.getNextNumber();
		}
		this.reportTemperature= gd.getNextNumber();
		this.showLegacy= gd.getNextBoolean();
		return true;
		}
		/* ======================================================================== */

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