implemented post-UV manual adjustment control (12670bc5) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+35 −0

Original line number	Diff line number	Diff line
		@@ -9983,11 +9983,19 @@ if (MORE_BUTTONS) {
		}
		// double [] targetTilts={0.0,0.0};
		double [] manualScrewsCW=null;
		double [] postUVScrews=null;
		if (zTxTyM1M2M3!=null){
		manualScrewsCW=FOCUSING_FIELD.fieldFitting.mechanicalFocusingModel.getManualScrews(
		zTxTy[0]-FOCUSING_FIELD.targetRelFocalShift, //double zErr, // positive - away from lens
		zTxTy[1]-FOCUSING_FIELD.targetRelTiltX, //targetTilts[0], // double tXErr,// positive - 1,2 away from lens, 3 - to the lens
		zTxTy[2]-FOCUSING_FIELD.targetRelTiltY); //targetTilts[1]); // double tYErr);

		postUVScrews=FOCUSING_FIELD.fieldFitting.mechanicalFocusingModel.getManualScrews(
		FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity,
		zTxTy[0]-FOCUSING_FIELD.targetRelFocalShift, //double zErr, // positive - away from lens
		zTxTy[1]-FOCUSING_FIELD.targetRelTiltX, //targetTilts[0], // double tXErr,// positive - 1,2 away from lens, 3 - to the lens
		zTxTy[2]-FOCUSING_FIELD.targetRelTiltY); //targetTilts[1]); // double tYErr);

		}
		double scaleMovement=1.0; // calculate automatically - reduce when close
		boolean parallelMove=false;
		@@ -10011,6 +10019,16 @@ if (MORE_BUTTONS) {
		else System.out.println("Suggested rotation for screw # "+(i+1)+
		" "+IJ.d2s(manualScrewsCW[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
		}
		if (postUVScrews!=null) {
		System.out.println("----- Post-UV fixture screw adjustments -----");
		for (int i=0;i<postUVScrews.length;i++){
		double deg=360*Math.abs(postUVScrews[i]);
		if (postUVScrews[i]>=0) System.out.println("Suggested rotation for screw # "+(i+1)+
		" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)");
		else System.out.println("Suggested rotation for screw # "+(i+1)+
		" "+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());
		@@ -10042,6 +10060,17 @@ 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)");
		}
		if (postUVScrews!=null) {
		for (int i=0;i<postUVScrews.length;i++){
		double deg=360*Math.abs(postUVScrews[i]);
		if (postUVScrews[i]>=0) gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CW)");
		else gd.addMessage("Screw # "+(i+1)+" "+IJ.d2s(postUVScrews[i],3)+" ("+IJ.d2s(deg,0)+"\u00b0 CCW)");
		}
		gd.addMessage( "--- Post-UV fixture screws sensitivity ---");
		for (int i=0;i<FOCUS_MEASUREMENT_PARAMETERS.postUVscrewSensitivity.length;i++){
		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

		@@ -10076,6 +10105,12 @@ if (MORE_BUTTONS) {
		newMotors[0]= (int) gd.getNextNumber();
		newMotors[1]= (int) gd.getNextNumber();
		newMotors[2]= (int) gd.getNextNumber();

		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();

src/main/java/FocusingField.java

+39 −0

Original line number	Diff line number	Diff line
		@@ -8631,6 +8631,45 @@ public boolean LevenbergMarquardt(
		return turnCW;
		}

		/**
		* Post UV gluing fixture adjustment, screw numbers match motor numbers
		* @param umPerTurn sensitivity of the 3 adjustment screws - microns of the uv-glued support movement per screw revolution
		* @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)
		* @return array of optimal CW rotations of each screw (1.0 == 360 deg)
		*/
		public double [] getManualScrews(
		double [] umPerTurn, // if null - use defined here
		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, up, thread pitch (pull) !!! Inverting Y! - again invert? 1 - far left, 2 - near left, 3 - right
		{ -13.5, -6.5, 192.8}, // -2.908571735}, // 192.8, ... for proto push-away fixture
		{ -13.5, 6.5, 202.6}, // -3.8198374024},
		{ 13.6, 3.5, 83.4}}; // -2.4491867448}};
		if (umPerTurn!=null) for (int i=0;i<umPerTurn.length;i++) screws[i][2]=umPerTurn[i];
		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]=moveDownUm[i]/screws[i][2];
		}
		return turnCW;
		}
		/*
		*
		192.8479341564
		202.5779753086
		83.4354504792

		-2.908571735
		-3.8198374024
		-2.4491867448

		*/

		/**
		* Calculate three linearized values of motor positions for current parameters, target center focal
		* shift and tilt (from the optic axis)

src/main/java/LensAdjustment.java

+25 −7

Original line number	Diff line number	Diff line
		@@ -255,18 +255,18 @@ public class LensAdjustment {
		// when approximating PSF with a second degree polynomial:
		public double psf_cutoffEnergy=0.98; //0.5; // disregard pixels outside of this fraction of the total energy
		public double psf_cutoffLevel= 0.2; // disregard pixels below this fraction of the maximal value
		public int psf_minArea = 10; // continue increasing the selected area, even if beyound psf_cutoffEnergy and psf_cutoffLevel,
		// if the selected area is smaller than this (so approximation wpuld work)
		public int psf_minArea = 10; // continue increasing the selected area, even if beyond psf_cutoffEnergy and psf_cutoffLevel,
		// if the selected area is smaller than this (so approximation would work)
		public double psf_blurSigma = 0.0; // optionally blur the calculated mask

		public double weightRatioRedToGreen=0.7; // Use this data when combining defocusing data from different color PSF
		public double weightRatioBlueToGreen=0.3;
		public double targetFarNear=0.0; // OBSOLETE target logariphm of average tangential-to-radial resolution
		public double weightRatioBlueToGreen=0.2;
		public double targetFarNear=0.0; // OBSOLETE target logarithm of average tangential-to-radial resolution
		public boolean useRadialTangential=false; // Use targetFarNear (radial/tangential resolution) as a proxy for the distance
		public double targetMicrons=0.0; // target lens center distance (away from "best focus"
		public double toleranceMicrons=0.5; // microns
		public double toleranceTilt=0.02; //
		public double toleranceThreshold=3.0; // When each error is under swcaled thereshold, reduce correxction step twice
		public double toleranceThreshold=3.0; // When each error is under scaled threshold, reduce correction step twice
		// public boolean parallelAdjust=true; // move 3 motors parallel after each 3-motor focus/tilt adjustment
		public double parallelAdjustThreshold=4.0; // adjust 3 motors parallel if focal distance error in the center exceeds this

		@@ -353,7 +353,7 @@ public class LensAdjustment {
		public int subdiv=4;
		// overwrites public static class MultiFilePSF.overexposedMaxFraction
		public double overexposedMaxFraction=0.1; // allowed fraction of the overexposed pixels in the PSF kernel measurement area
		// overwirites public static class PSFParameters.minDefinedArea
		// overwrites public static class PSFParameters.minDefinedArea
		public double minDefinedArea=0.75; // minimal (weighted) fraction of the defined patter pixels in the FFT area
		public int PSFKernelSize=32; // size of the detected PSF kernel
		public boolean approximateGrid=true; // approximate grid with polynomial
		@@ -375,6 +375,7 @@ public class LensAdjustment {
		public double correlationMinAbsoluteContrast=0.5; // minimal contrast for the pattern to pass, does not compensate for low ligt
		public double correlationMinAbsoluteInitialContrast=0.5; // minimal contrast for the pattern of the center (initial point)

		public double [] postUVscrewSensitivity={-2.908571735,-3.8198374024,-2.4491867448};

		public boolean flatFieldCorrection=true;
		public double flatFieldExpand=4.0;
		@@ -597,6 +598,7 @@ public class LensAdjustment {
		double correlationMinInitialContrast, // minimal contrast for the pattern of the center (initial point)
		double correlationMinAbsoluteContrast, // minimal contrast for the pattern to pass, does not compensate for low ligt
		double correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point)
		double [] postUVscrewSensitivity, // microns/turn for 3 post-UV fixture adjustment screws
		boolean flatFieldCorrection,
		double flatFieldExpand,
		double thresholdFinish,// (copied from series) stop iterations if 2 last steps had less improvement (but not worsening )
		@@ -752,6 +754,7 @@ public class LensAdjustment {
		this.correlationMinInitialContrast=correlationMinInitialContrast; // minimal contrast for the pattern of the center (initial point)
		this.correlationMinAbsoluteContrast=correlationMinAbsoluteContrast; // minimal contrast for the pattern to pass, does not compensate for low ligt
		this.correlationMinAbsoluteInitialContrast=correlationMinAbsoluteInitialContrast; // minimal contrast for the pattern of the center (initial point)
		this.postUVscrewSensitivity=postUVscrewSensitivity.clone(); // microns/turn for 3 post-UV fixture adjustment screws
		this.flatFieldCorrection=flatFieldCorrection;
		this.flatFieldExpand=flatFieldExpand;
		this.thresholdFinish=thresholdFinish;// (copied from series) stop iterations if 2 last steps had less improvement (but not worsening )
		@@ -910,6 +913,7 @@ public class LensAdjustment {
		this.correlationMinInitialContrast,
		this.correlationMinAbsoluteContrast,
		this.correlationMinAbsoluteInitialContrast,
		this.postUVscrewSensitivity,
		this.flatFieldCorrection,
		this.flatFieldExpand,
		this.thresholdFinish,
		@@ -1078,7 +1082,9 @@ public class LensAdjustment {
		properties.setProperty(prefix+"correlationMinInitialContrast",this.correlationMinInitialContrast+"");
		properties.setProperty(prefix+"correlationMinAbsoluteContrast",this.correlationMinAbsoluteContrast+"");
		properties.setProperty(prefix+"correlationMinAbsoluteInitialContrast",this.correlationMinAbsoluteInitialContrast+"");

		for (int i=0;i<this.postUVscrewSensitivity.length;i++){
		properties.setProperty(prefix+"postUVscrewSensitivity_"+i,this.postUVscrewSensitivity[i]+"");
		}
		properties.setProperty(prefix+"flatFieldCorrection",this.flatFieldCorrection+"");
		properties.setProperty(prefix+"flatFieldExpand",this.flatFieldExpand+"");
		properties.setProperty(prefix+"thresholdFinish",this.thresholdFinish+"");
		@@ -1405,6 +1411,10 @@ public class LensAdjustment {
		this.correlationMinAbsoluteContrast=Double.parseDouble(properties.getProperty(prefix+"correlationMinAbsoluteContrast"));
		if (properties.getProperty(prefix+"correlationMinAbsoluteInitialContrast")!=null)
		this.correlationMinAbsoluteInitialContrast=Double.parseDouble(properties.getProperty(prefix+"correlationMinAbsoluteInitialContrast"));
		for (int i=0;i<this.postUVscrewSensitivity.length;i++){
		if (properties.getProperty(prefix+"postUVscrewSensitivity_"+i)!=null)
		this.postUVscrewSensitivity[i]=Double.parseDouble(properties.getProperty(prefix+"postUVscrewSensitivity_"+i));
		}
		if (properties.getProperty(prefix+"flatFieldCorrection")!=null)
		this.flatFieldCorrection=Boolean.parseBoolean(properties.getProperty(prefix+"flatFieldCorrection"));
		if (properties.getProperty(prefix+"flatFieldExpand")!=null)
		@@ -1679,6 +1689,11 @@ public class LensAdjustment {
		gd.addNumericField("Expand during extrapolation (relative to the average grid period)", this.flatFieldExpand, 3);
		gd.addNumericField("Threshold RMS to exit LMA", this.thresholdFinish, 7,9,"pix");
		gd.addNumericField("Maximal number of LMA iterations per series",this.numIterations, 0);
		gd.addMessage( "--- Post-UV fixture screws sensitivity ---");
		for (int i=0;i<this.postUVscrewSensitivity.length;i++){
		gd.addNumericField("Screw "+i+" sensitivity", this.postUVscrewSensitivity[i], 4,6,"um/turn CW");
		}

		gd.addMessage("-----");
		gd.addNumericField("Report focal length at this temperature", this.reportTemperature, 1,5,"C");

		@@ -1869,6 +1884,9 @@ public class LensAdjustment {
		this.flatFieldExpand= gd.getNextNumber();
		this.thresholdFinish= gd.getNextNumber();
		this.numIterations= (int) gd.getNextNumber();
		for (int i=0;i<this.postUVscrewSensitivity.length;i++){
		this.postUVscrewSensitivity[i]= gd.getNextNumber();
		}
		this.reportTemperature= gd.getNextNumber();
		return true;
		}

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