Added suggestions for manual screws (handling motors out of range) (f8cffed4) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+65 −2

Original line number	Diff line number	Diff line
		@@ -4544,6 +4544,12 @@ if (MORE_BUTTONS) {
		return;
		}
		}
		// Just for old focal distance calculation
		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
		FOCUS_MEASUREMENT_PARAMETERS,
		MOTORS.getMicronsPerStep(), //double micronsPerStep,
		DEBUG_LEVEL);

		while (adjustFocusTiltLMA());
		return;
		}
		@@ -8698,10 +8704,12 @@ if (MORE_BUTTONS) {
		/* ===== Other methods ==================================================== */
		public boolean adjustFocusTiltLMA(){
		// just for reporting distance old way
		/*
		MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
		FOCUS_MEASUREMENT_PARAMETERS,
		MOTORS.getMicronsPerStep(), //double micronsPerStep,
		DEBUG_LEVEL);
		*/
		// No-move measure, add to history
		moveAndMaybeProbe(
		true, // just move, not probe
		@@ -8724,7 +8732,7 @@ if (MORE_BUTTONS) {
		//get measurement
		FocusingField.FocusingFieldMeasurement fFMeasurement=MOTORS.getThisFFMeasurement(FOCUSING_FIELD);
		// calculate z, tx, ty, m1,m2,m3
		double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA (fFMeasurement);
		double [] zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(fFMeasurement,false);
		// show dialog: Apply, re-calculate, exit
		int [] currentMotors=fFMeasurement.motors;
		int [] newMotors=currentMotors.clone();
		@@ -8738,15 +8746,47 @@ if (MORE_BUTTONS) {
		zTxTy[2]=zTxTyM1M2M3[2];
		}
		double [] targetTilts={0.0,0.0};
		double [] manualScrewsCW=null;
		if (zTxTyM1M2M3!=null){
		manualScrewsCW=FOCUSING_FIELD.fieldFitting.mechanicalFocusingModel. getManualScrews(
		zTxTy[0]-FOCUSING_FIELD.targetRelFocalShift, //double zErr, // positive - away from lens
		zTxTy[1]-targetTilts[0], // double tXErr,// positive - 1,2 away from lens, 3 - to the lens
		zTxTy[2]-targetTilts[1]); // double tYErr);
		}
		double scaleMovement=1.0; // calculate automatically - reduce when close
		boolean parallelMove=false;
		if (MASTER_DEBUG_LEVEL>0){
		System.out.println("----- Focus/tilt measurement results -----");
		System.out.println("Relative focal shift "+IJ.d2s(zTxTy[0],3)+" um ("+IJ.d2s(FOCUSING_FIELD.targetRelFocalShift,3)+"um)");
		System.out.println("Horizontal tilt "+IJ.d2s(zTxTy[1],3)+" um/mm ("+IJ.d2s(targetTilts[0],3)+"um/mm)");
		System.out.println("Vertical tilt "+IJ.d2s(zTxTy[2],3)+" um/mm ("+IJ.d2s(targetTilts[1],3)+"um/mm)");
		for (int i=0;i<newMotors.length;i++){
		System.out.println("Suggested for motor "+(i+1)+" "+newMotors[i]+" ("+currentMotors[i]+")");
		}
		if (manualScrewsCW!=null) for (int i=0;i<manualScrewsCW.length;i++){
		if (manualScrewsCW[i]>=0) System.out.println("Suggested rotation for screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" (CW)");
		else System.out.println("Suggested rotation for screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" (CCW)");
		}
		System.out.println("----- end of Focus/tilt measurement results -----");
		}
		GenericDialog gd = new GenericDialog("Adjusting focus/tilt");
		if (zTxTyM1M2M3==null){
		gd.addMessage("** Failed to determine focus/tilt, probably too far out of focus. **");
		gd.addMessage("** You may cancel the command and try \"Auto pre-focus\" first. **");
		}
		gd.addNumericField("Target focus (relative to best composirte)",FOCUSING_FIELD.targetRelFocalShift,2,5,"um ("+IJ.d2s(zTxTy[0],3)+")");
		gd.addNumericField("Target horizontal tilt (normally 0)",targetTilts[0],2,5,"um/mm ("+IJ.d2s(zTxTy[1],3)+")");
		gd.addNumericField("Target vertical tilt (normally 0)",targetTilts[1],2,5,"um/mm ("+IJ.d2s(zTxTy[2],3)+")");
		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]+")");
		gd.addMessage("Suggested rotation of the top screws, use if motor positions are out of limits - outside of +/-25,000");
		if (manualScrewsCW!=null) for (int i=0;i<manualScrewsCW.length;i++){
		if (manualScrewsCW[i]>=0) gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" (CW)");
		else gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(manualScrewsCW[i],3)+" (CCW)");
		}
		gd.addNumericField("Scale movement",scaleMovement,3,5,"x");
		gd.addCheckbox("Recalculate and apply parallel move only",parallelMove); // should be false after manual movement

		gd.addCheckbox("Filter samples/channels by Z",FOCUSING_FIELD.filterZ); // should be false after manual movement
		gd.addCheckbox("Filter by value (leave lower than maximal fwhm used in focal scan mode)",FOCUSING_FIELD.filterByScanValue);
		@@ -8773,7 +8813,7 @@ if (MORE_BUTTONS) {
		newMotors[1]= (int) gd.getNextNumber();
		newMotors[2]= (int) gd.getNextNumber();
		scaleMovement= gd.getNextNumber();

		parallelMove= gd.getNextBoolean();
		FOCUSING_FIELD.filterZ= gd.getNextBoolean();
		FOCUSING_FIELD.filterByScanValue= gd.getNextBoolean();
		FOCUSING_FIELD.filterByValueScale= gd.getNextNumber();
		@@ -8789,6 +8829,18 @@ if (MORE_BUTTONS) {
		MASTER_DEBUG_LEVEL=( int) gd.getNextNumber();
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
		if (parallelMove){ // ignore/recalculate newMotors data
		zTxTyM1M2M3 = FOCUSING_FIELD.adjustLMA(fFMeasurement,true); // recalculate with parallel move only
		newMotors=currentMotors.clone();
		if (zTxTyM1M2M3!=null){
		newMotors[0]=(int) Math.round(zTxTyM1M2M3[3]);
		newMotors[1]=(int) Math.round(zTxTyM1M2M3[4]);
		newMotors[2]=(int) Math.round(zTxTyM1M2M3[5]);
		}
		System.out.println("Parallel move position for motor 1 "+newMotors[0]+" ("+currentMotors[0]+")");
		System.out.println("Parallel move position for motor 2 "+newMotors[1]+" ("+currentMotors[1]+")");
		System.out.println("Parallel move position for motor 3 "+newMotors[2]+" ("+currentMotors[2]+")");
		}

		// Scale motor movement
		newMotors[0]=currentMotors[0]+((int) Math.round((newMotors[0]-currentMotors[0])*scaleMovement));
		@@ -10042,6 +10094,7 @@ if (MORE_BUTTONS) {
		return null;
		}
		if (allOK) {
		if (focusMeasurementParameters.scanMeasureLast) {
		allOK &= moveAndMaybeProbe(
		true,
		centerMotorPos, // null OK
		@@ -10060,6 +10113,16 @@ if (MORE_BUTTONS) {
		updateStatus,
		debugLevel,
		loopDebugLevel);
		} else { // just move, no measuring
		System.out.println("Returning motors to initial position at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		focusingMotors.moveElphel10364Motors( // return to last direct scan position
		true, //boolean wait,
		centerMotorPos,
		0.0, //double sleep,
		true, //boolean showStatus,
		"", //String message,
		false); //focusMeasurementParameters.compensateHysteresis); //boolean hysteresis)
		}
		}

		if (debugLevel>0) System.out.println("Scanning focus in the center, number of steps="+ focusMeasurementParameters.scanNumber+

src/main/java/FocusingField.java

+63 −3

Original line number	Diff line number	Diff line
		@@ -4255,6 +4255,7 @@ public boolean LevenbergMarquardt(
		}
		}
		double [] dmz= getAdjustedMotors(
		null, // double [] zM0, // current linearized motors (or null for full adjustment)
		targetRelFocalShift+best_qb_corr[0],
		targetTiltX, // for testing, normally should be 0 um/mm
		targetTiltY,
		@@ -4263,6 +4264,7 @@ public boolean LevenbergMarquardt(
		System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));
		}
		double [] dm= getAdjustedMotors(
		null, // double [] zM0, // current linearized motors (or null for full adjustment)
		targetRelFocalShift+best_qb_corr[0],
		targetTiltX, // for testing, normally should be 0 um/mm
		targetTiltY,
		@@ -4312,6 +4314,7 @@ public boolean LevenbergMarquardt(
		}
		}
		double [] dmz= getAdjustedMotors(
		null, // double [] zM0, // current linearized motors (or null for full adjustment)
		targetRelFocalShift+best_qb_corr[0],
		targetTiltX, // for testing, normally should be 0 um/mm
		targetTiltY,
		@@ -4320,6 +4323,7 @@ public boolean LevenbergMarquardt(
		System.out.println("Suggested motor linearized positions: "+IJ.d2s(dmz[0],2)+":"+IJ.d2s(dmz[1],2)+":"+IJ.d2s(dmz[2],2));
		}
		double [] dm= getAdjustedMotors(
		null, // double [] zM0, // current linearized motors (or null for full adjustment)
		targetRelFocalShift+best_qb_corr[0],
		targetTiltX, // for testing, normally should be 0 um/mm
		targetTiltY,
		@@ -4369,7 +4373,9 @@ public boolean LevenbergMarquardt(
		}

		//,
		public double [] adjustLMA (FocusingFieldMeasurement measurement){
		public double [] adjustLMA (
		FocusingFieldMeasurement measurement,
		boolean parallelMove){
		if (!testMeasurement(
		measurement,
		zMin, //+best_qb_corr[0],
		@@ -4390,7 +4396,13 @@ public boolean LevenbergMarquardt(
		result[0]=zTilts[0]-best_qb_corr[0];
		result[1]=zTilts[1];
		result[2]=zTilts[2];
		double [] zm=null;
		if (parallelMove){
		zm=new double [3];
		for (int i=0;i<zm.length;i++) zm[i]=fieldFitting.mechanicalFocusingModel.mToZm(measurement.motors[i], i);
		}
		double [] dm= getAdjustedMotors(
		zm,
		targetRelFocalShift+best_qb_corr[0],
		0.0, // targetTiltX, // for testing, normally should be 0 um/mm
		0.0, // targetTiltY,
		@@ -4426,11 +4438,13 @@ public boolean LevenbergMarquardt(
		}

		public double [] getAdjustedMotors(
		double [] zM0, // current linearized motors (or null for full adjustment)
		double targetRelFocalShift,
		double targetTiltX, // for testing, normally should be 0 um/mm
		double targetTiltY, // for testing, normally should be 0 um/mm
		boolean motorSteps){
		double [] zM=fieldFitting.mechanicalFocusingModel.getZM(
		zM0,
		currentPX0, //fieldFitting.getCenterXY()[0],
		currentPY0, //fieldFitting.getCenterXY()[1],
		targetRelFocalShift,
		@@ -4516,7 +4530,7 @@ public boolean LevenbergMarquardt(
		break;
		}
		if (!changedEnable) {
		if (debugLevel>0) System.out.println("No filter chnage, finished in "+(n+1)+" steps");
		if (debugLevel>0) System.out.println("No filter cnange, finished in "+(n+1)+" step"+((n==0)?"":"s"));
		return true;
		} else {
		if ((was2PrevEnable!=null) && (prevEnable!=null) && (was2PrevEnable.length==prevEnable.length)){
		@@ -4541,7 +4555,7 @@ public boolean LevenbergMarquardt(
		private double [] pXY=null;
		private boolean [] centerSelect=null;
		private boolean [] centerSelectDefault={true,true};
		private MechanicalFocusingModel mechanicalFocusingModel;
		public MechanicalFocusingModel mechanicalFocusingModel;
		private CurvatureModel [] curvatureModel=new CurvatureModel[6]; // 3 colors, sagittal+tangential each
		private boolean [] channelSelect=null;
		private boolean [] mechanicalSelect=null;
		@@ -6609,9 +6623,44 @@ public boolean LevenbergMarquardt(
		}
		return m;
		}
		/**
		* Calculate manual screw adjustments for focus/tilt to reduce amount of motor travel (when it is out of limits)
		* @param zErr current focal distance error in microns, positive - away from lens
		* @param tXErr current horizontal tilt in microns/mm , positive - 1,2 away from lens, 3 - to the lens
		* @param tYErr current vertical tilt in microns/mm , positive - 2 away from lens, 1 - to the lens
		* @return array of optimal CW rotations of each screw (1.0 == 360 deg)
		* Screw locations:
		* 5 2
		* 3 +
		* 4 1
		* + - center
		* 1,2 M2x0.4 set screws (push)
		* 3 - M2x0.4 socket screw (push)
		* 4 - M2x0.4 socket screw (pull)
		* 5 - M2.5x0.45 screw (pull)
		*/
		public double [] getManualScrews(
		double zErr, // positive - away from lens
		double tXErr,// positive - 1,2 away from lens, 3 - to the lens
		double tYErr){// positive - 2 away from lens
		double [][] screws={ // right, down, thread pitch (pull)
		{ 20.5 ,17.5, -0.4},
		{ 20.5,-17.5, -0.4},
		{-20.5, 0.0, -0.4},
		{ 0.0, 17.5, 0.4},
		{ 0.0,-17.5, 0.45}};
		double [] moveDownUm=new double [screws.length];
		double [] turnCW=new double [screws.length];
		for (int i=0;i<screws.length;i++){
		moveDownUm[i]=zErr + screws[i][0]tXErr+screws[i][1]tYErr;
		turnCW[i]=0.001*moveDownUm[i]/screws[i][2];
		}
		return turnCW;
		}

		/**
		* Calculate three linearized values of motor positions for current parameters, target center focal shift and tilt
		* @param zM0 current linearized position (for parallel adjustment) or null for full adjustment
		* @param px lens center X (pixels)
		* @param py lens center Y (pixels)
		* @param targetZ target focal shift uin the center, microns, positive - away
		@@ -6620,6 +6669,7 @@ public boolean LevenbergMarquardt(
		* @return array of 3 linearized motor positions (microns)
		*/
		public double [] getZM(
		double [] zMCurrent, // current linearized motors (or null for full adjustment)
		double px,
		double py,
		double targetZ,
		@@ -6627,6 +6677,16 @@ public boolean LevenbergMarquardt(
		double targetTy){
		double dx=PIXEL_SIZE*(px-getValue(MECH_PAR.mpX0));
		double dy=PIXEL_SIZE*(py-getValue(MECH_PAR.mpY0));
		if (zMCurrent!=null){
		// 0.25* zM1+ 0.25* zM2+ 0.5 * zM3 = targetZ-getValue(MECH_PAR.z0);
		// 0.25* (zM1+dzM)+ 0.25* (zM2+dzM)+ 0.5 * (zM3+dzM) = targetZ-getValue(MECH_PAR.z0);
		// 0.25* (dzM+ 0.25* dzM+ 0.5 * dzM = targetZ-getValue(MECH_PAR.z0) - (0.25* zM1+ 0.25* zM2+ 0.5 * zM3 );
		// dzM = targetZ-getValue(MECH_PAR.z0) - (0.25* zM1+ 0.25* zM2+ 0.5 * zM3 );
		double dZM=targetZ-getValue(MECH_PAR.z0)-(0.25* zMCurrent[0]+ 0.25* zMCurrent[1]+ 0.5 * zMCurrent[2]);
		double [] zM=zMCurrent.clone();
		for (int i=0;i<zM.length;i++) zM[i]+=dZM;
		return zM;
		}
		// double zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3+getValue(MECH_PAR.z0);
		// double zx=dx(getValue(MECH_PAR.tx)+(2zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))) ;
		// double zy=dy(getValue(MECH_PAR.ty)-(zM2-zM1)/(2getValue(MECH_PAR.Ly)));//!

src/main/java/LensAdjustment.java

+14 −8

Original line number	Diff line number	Diff line
		@@ -305,6 +305,7 @@ public class LensAdjustment {

		public boolean scanTiltEnable=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
		public int scanTiltRangeY=14336; // 4 periods
		public int scanTiltStepsX=24;
		@@ -520,6 +521,7 @@ public class LensAdjustment {

		boolean scanTiltEnable, //=true; // enable scanning tilt
		boolean scanTiltReverse,
		boolean scanMeasureLast,
		int scanTiltRangeX, //=14336; // 4 periods
		int scanTiltRangeY, //=14336; // 4 periods
		int scanTiltStepsX, //=24;
		@@ -663,6 +665,7 @@ public class LensAdjustment {

		this.scanTiltEnable=scanTiltEnable; //=true; // enable scanning tilt
		this.scanTiltReverse=scanTiltReverse;
		this.scanMeasureLast=scanMeasureLast;
		this.scanTiltRangeX=scanTiltRangeX; //, //=14336; // 4 periods
		this.scanTiltRangeY=scanTiltRangeY; //, //=14336; // 4 periods
		this.scanTiltStepsX=scanTiltStepsX; //=24;
		@@ -807,6 +810,7 @@ public class LensAdjustment {

		this.scanTiltEnable, // enable scanning tilt
		this.scanTiltReverse,
		this.scanMeasureLast,
		this.scanTiltRangeX, // 4 periods
		this.scanTiltRangeY, // 4 periods
		this.scanTiltStepsX,
		@@ -952,24 +956,18 @@ public class LensAdjustment {
		properties.setProperty(prefix+"scanStep",this.scanStep+"");
		properties.setProperty(prefix+"scanNumber",this.scanNumber+"");
		properties.setProperty(prefix+"scanNumberNegative",this.scanNumberNegative+"");

		properties.setProperty(prefix+"scanHysteresis",this.scanHysteresis+"");
		properties.setProperty(prefix+"scanHysteresisNumber",this.scanHysteresisNumber+"");

		properties.setProperty(prefix+"scanTiltEnable",this.scanTiltEnable+""); // enable scanning tilt
		properties.setProperty(prefix+"scanTiltReverse",this.scanTiltReverse+"");

		properties.setProperty(prefix+"scanMeasureLast",this.scanMeasureLast+"");
		properties.setProperty(prefix+"scanTiltRangeX",this.scanTiltRangeX+""); // 4 periods
		properties.setProperty(prefix+"scanTiltRangeY",this.scanTiltRangeY+""); // 4 periods
		properties.setProperty(prefix+"scanTiltStepsX",this.scanTiltStepsX+"");
		properties.setProperty(prefix+"scanTiltStepsY",this.scanTiltStepsY+"");


		properties.setProperty(prefix+"motorHysteresis",this.motorHysteresis+"");
		properties.setProperty(prefix+"measuredHysteresis",this.measuredHysteresis+"");

		properties.setProperty(prefix+"motorCalm",this.motorCalm+"");

		properties.setProperty(prefix+"linearReductionRatio",this.linearReductionRatio+"");
		properties.setProperty(prefix+"motorDebug",this.motorDebug+"");
		properties.setProperty(prefix+"lensDistanceNumPoints",this.lensDistanceNumPoints+"");
		@@ -1217,6 +1215,9 @@ public class LensAdjustment {
		this.scanTiltReverse=Boolean.parseBoolean(properties.getProperty(prefix+"scanTiltReverse"));


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

		if (properties.getProperty(prefix+"scanTiltRangeX")!=null)
		this.scanTiltRangeX=Integer.parseInt(properties.getProperty(prefix+"scanTiltRangeX"));
		if (properties.getProperty(prefix+"scanTiltRangeY")!=null)
		@@ -1364,7 +1365,7 @@ public class LensAdjustment {

		gd.addCheckbox ("Scan for tilt measurement (approximately preserving center)", this.scanTiltEnable);
		gd.addCheckbox ("Scan for tilt measurement in both directions", this.scanTiltReverse);

		gd.addCheckbox ("Calculate PSF after returning to the initial position", this.scanMeasureLast);

		gd.addNumericField("Full range of scanning motors tilting in X-direction", this.scanTiltRangeX, 0,7,"motors steps");
		gd.addNumericField("Full range of scanning motors tilting in Y-direction", this.scanTiltRangeY, 0,7,"motors steps");
		@@ -1386,6 +1387,8 @@ public class LensAdjustment {

		this.scanTiltEnable= gd.getNextBoolean();
		this.scanTiltReverse= gd.getNextBoolean();
		this.scanMeasureLast= gd.getNextBoolean();

		this.scanTiltRangeX= (int) gd.getNextNumber();
		this.scanTiltRangeY= (int) gd.getNextNumber();
		this.scanTiltStepsX= (int) gd.getNextNumber();
		@@ -1518,6 +1521,8 @@ public class LensAdjustment {

		gd.addCheckbox ("Scan for tilt measurement (approximately preserving center)", this.scanTiltEnable);
		gd.addCheckbox ("Scan for tilt measurement in both directions", this.scanTiltReverse);
		gd.addCheckbox ("Calculate PSF after returning to the initial position", this.scanMeasureLast);


		gd.addNumericField("Full range of scanning motors tilting in X-direction", this.scanTiltRangeX, 0,7,"motors steps");
		gd.addNumericField("Full range of scanning motors tilting in Y-direction", this.scanTiltRangeY, 0,7,"motors steps");
		@@ -1684,6 +1689,7 @@ public class LensAdjustment {

		this.scanTiltEnable= gd.getNextBoolean();
		this.scanTiltReverse= gd.getNextBoolean();
		this.scanMeasureLast= gd.getNextBoolean();
		this.scanTiltRangeX= (int) gd.getNextNumber();
		this.scanTiltRangeY= (int) gd.getNextNumber();
		this.scanTiltStepsX= (int) gd.getNextNumber();

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