implemented post-UV manual adjustment control

src/main/java/Aberration_Calibration.java

@@ -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

@@ -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

@@ -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;
     	}