modified other distance measurements (like for temperature coefficient)

to use lens aberration model

src/main/java/CalibrationHardwareInterface.java

@@ -2977,7 +2977,25 @@ public class CalibrationHardwareInterface {
     			fullResults
     	);
     }
+    
+	public FocusingField.FocusingFieldMeasurement getThisFFMeasurement(
+			FocusingField focusingField,
+			String sTimestamp,
+			double temperature,
+			double[][] psfMetrics,
+			double [][][][] fullResults){
+		
+		return focusingField.getFocusingFieldMeasurement(
+				sTimestamp,   //focusingState.getTimestamp(),
+				temperature, //focusingState.getTemperature(),
+				this.curpos,      //focusingState.motorsPos,
+				fullResults); //focusingState.getSamples());
+	}    
+    
+    
+    
 /*
+ * FocusingHistory.FocusingState focusingState
     public void addToHistory( String sTimestamp,double temperature, double[][] psfMetrics){ // null OK
     	this.focusingHistory.add(
     			sTimestamp,
@@ -3004,6 +3022,7 @@ public class CalibrationHardwareInterface {
     }
 
     public void listHistory(
+    		boolean useLMA,
     		String path,
     		String lensSerial,
     		String comment,
@@ -3015,6 +3034,7 @@ public class CalibrationHardwareInterface {
 			double weightY // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
 			){
     	listHistory(
+    			useLMA,
     			path,
     			"",
     			lensSerial,
@@ -3033,6 +3053,7 @@ public class CalibrationHardwareInterface {
     }
     
     public void listHistory(
+    		boolean useLMA,
     		String path,
     		String serialNumber,
     		String lensSerial,
@@ -3051,6 +3072,7 @@ public class CalibrationHardwareInterface {
 			){
 
     	this.focusingHistory.list(
+        		useLMA,
     			path,
         		serialNumber,
     			lensSerial,
@@ -3084,6 +3106,7 @@ public class CalibrationHardwareInterface {
     			pY0,
     			sampleCoord);
 	}
+
 	public FocusingField.FocusingFieldMeasurement getThisFFMeasurement(FocusingField focusingField){
 		return getThisFFMeasurement(focusingField, -1);
 	}    
@@ -3899,6 +3922,14 @@ public class CalibrationHardwareInterface {
     		if ((index<0) || (index>=this.history.size())) return null;
     		return this.history.get(index).getCenterResolutions();
     	}
+    	public double [] getzTxTy(int index){
+    		if ((index<0) || (index>=this.history.size())) return null;
+    		return this.history.get(index).getzTxTy();
+    	}
+    	public double [] getzTxTy(){
+    		if (this.history.size()<1) return null;
+    		return getzTxTy(this.history.size()-1);
+    	}
     	public int size(){
     		return this.history.size();
     	}
@@ -5067,6 +5098,7 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
  * @return array of 2 elements - {length at 0C, microns/degree}
  */
      	public double [] temperatureLinearApproximation(
+     			boolean useLMA,
      			int numSamples,             // number of last samples from history to use, 0 - use all
     			double lensDistanceWeightK, // used in distance calculation 
     			double lensDistanceWeightY // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
@@ -5079,8 +5111,11 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
     		int firstSample=this.history.size()-numSamples;
 
      		for (int nSample=0;nSample<numSamples;nSample++){
-				resolutions= this.history.get(firstSample+nSample).getCenterResolutions();
 				data[nSample][0]=this.history.get(firstSample+nSample).getTemperature();
+				if (useLMA){
+					data[nSample][1]=this.history.get(firstSample+nSample).getzTxTy()[0];
+				} else {
+					resolutions= this.history.get(firstSample+nSample).getCenterResolutions();
 					data[nSample][1]=getLensDistance(
 							resolutions, // {R-sharpness,G-sharpness,B-sharpness}
 							true, // boolean absolute, // return absolutely calibrated data
@@ -5089,6 +5124,7 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
 							1 //debugLevel
 							);
 				}
+     		}
 			PolynomialApproximation pa= new PolynomialApproximation(debugLevel);
 			double [] polyCoeff=pa.polynomialApproximation1d(data, 1); // just linear
 			return polyCoeff;
@@ -5524,6 +5560,7 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
     	// todo - add "probe around" - 6/3 points, +/- for each direction (fraction of sigma?)    	    	
 
     	public void list(
+    			boolean useLMA,
     			String path,
     			String lensSerial, // if null - do not add average
         		String comment,
@@ -5533,8 +5570,10 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
     			double weightRatioBlueToGreen,
     			double weightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives 
     			double weightY){ // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
-    		list (path,
-    				"",
+    		list (
+    				useLMA,
+    				path,
+    				"", // serial; number
     				lensSerial, // if null - do not add average
     				comment,
     				showIndividualComponents,
@@ -5641,6 +5680,7 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
         	 
     	}
      	public void list(
+        		boolean useLMA,
     			String path,
         		String serialNumber,
     			String lensSerial, // if null - do not add average
@@ -5701,15 +5741,22 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
     		if (showIndividualComponents) {
     			for (int i=0;i<this.history.size();i++){
     				FocusingState focusingState=this.history.get(i);
+    				double [] zTxTy=useLMA?focusingState.getzTxTy():null;
     				double [][] metrics=focusingState.getMetrics(weightRatioRedToGreen,weightRatioBlueToGreen);
     				double [][] resolution=focusingState.getSharpness(weightRatioRedToGreen,weightRatioBlueToGreen);
-    				double dist= getLensDistance(
+    				double dist= (zTxTy==null)?getLensDistance(
     						focusingState.getCenterResolutions(), // {R-sharpness,G-sharpness,B-sharpness}
     		    			true, //boolean absolute, // return absolutely calibrated data
     		    			weightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives 
     		    			weightY, // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
-    		    			1); //int debugLevel
+    		    			1): //int debugLevel
+    		    				zTxTy[0];
     				double []   averageMetrics=metrics[3];
+    				if (zTxTy!=null){
+        				averageMetrics=metrics[3].clone(); // to modify w/o changing original
+    					averageMetrics[1]=zTxTy[1]; // tiltX
+    					averageMetrics[2]=zTxTy[2]; // tiltY
+    				}
     				double []   averageResolution=resolution[3];
     				sb.append((i+1)+"\t");
     				String timestamp=focusingState.getTimestamp();
@@ -5779,9 +5826,15 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
     			for (int i=0;i<this.history.size();i++){
 //    				int parIndex=0;
     				FocusingState focusingState=this.history.get(i);
+    				double [] zTxTy=useLMA?focusingState.getzTxTy():null;
     				double [][] metrics=focusingState.getMetrics(weightRatioRedToGreen,weightRatioBlueToGreen);
     				double [][] resolution=focusingState.getSharpness(weightRatioRedToGreen,weightRatioBlueToGreen);
     				double []   averageMetrics=metrics[3];
+    				if (zTxTy!=null){
+        				averageMetrics=metrics[3].clone(); // to modify w/o changing original
+    					averageMetrics[1]=zTxTy[1]; // tiltX
+    					averageMetrics[2]=zTxTy[2]; // tiltY
+    				}
     				double []   averageResolution=resolution[3];
     				if (!justSummary) sb.append((i+1)+"\t");
     				String timestamp=focusingState.getTimestamp();
@@ -5806,12 +5859,13 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
 					sums[4]+=focusingState.motorsPos[0];
 					sums[5]+=focusingState.motorsPos[1];
 					sums[6]+=focusingState.motorsPos[2];
-    				double dist= getLensDistance(
+					double dist= (zTxTy==null)?getLensDistance(
 							focusingState.getCenterResolutions(), // {R-sharpness,G-sharpness,B-sharpness}
 							true, //boolean absolute, // return absolutely calibrated data
 							weightK, // 0.0 - all 3 component errors are combined with the same weights. 1.0 - proportional to squared first derivatives 
 							weightY, // R-frac, Y-frac have the same scale regardless of the sharpness, but not Y. This is to balance Y contribution
-    		    			1); //int debugLevel
+							1): //int debugLevel
+								zTxTy[0];
     				if (Double.isNaN(dist)){
     					if (!justSummary) sb.append("\t---");
     				} else {
@@ -6199,7 +6253,19 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
     					1.0,
     					weightRatioBlueToGreen);
     		}
+    		// alternative mode (from aberration model) ising metrics[6][]
+    		public double [] getzTxTy(){
+    			if (this.psfMetricses==null){
+    				return null;
+    			}
+    			if ((this.psfMetricses.length<7) || (this.psfMetricses[6]==null)) {
+    				System.out.println("BUG? psfMetrics does not have line 6 with lens berration model z, tx, ty");
+    				return null;
+    			}
+    			double [] zTxTy={this.psfMetricses[6][0],this.psfMetricses[6][1],this.psfMetricses[6][2]};
+    			return zTxTy;
 
+    		}
     		public double [][] getMetrics(
     				double weightRed,
     				double weightGreen,

src/main/java/FocusingField.java

@@ -5121,20 +5121,39 @@ public boolean LevenbergMarquardt(
     
     public double [][] getAllZTM(
     		boolean noTiltScan,
-    		FocusingField ff){
-    	double [][] result =new double[ff.measurements.size()][6];
-    	for (int i=0;i<result.length;i++) result[i]=adjustLMA(noTiltScan,ff.measurements.get(i),false);
+    		FocusingField ff,
+    		boolean noMotors){
+    	double [][] result =new double[ff.measurements.size()][];
+    	for (int i=0;i<result.length;i++) result[i]=adjustLMA(
+    			noTiltScan,
+    			ff.measurements.get(i),
+				false, // boolean parallelMove,
+				true, // boolean noQualB,   // do not re-claculate testQualB 
+				noMotors); // boolean noAdjust) // do not calculate correction
     	return result;
     }
 
     public double [] averageZTM(// results relative to optimal
     		boolean noTiltScan,
-    		FocusingField ff){
-    	double [] result =new double[6];
+    		FocusingField ff,
+    		boolean noMotors){
+		if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode);
+		testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
+		if (debugLevel>0) {
+			System.out.println("Optimal absolute Zc="+this.qualBOptimizationResults[0]);
+			System.out.println("Optimal Tx="+this.qualBOptimizationResults[1]);
+			System.out.println("Optimal Ty="+this.qualBOptimizationResults[2]);
+		}
+    	double [] result =new double[noMotors?3:6];
     	for (int i=0;i<result.length;i++) result[i]=0.0;
     	int num=0;
     	for (FocusingFieldMeasurement measurement:ff.measurements){
-    		double [] ZTM = adjustLMA(noTiltScan,measurement,false);
+    		double [] ZTM = adjustLMA(
+    				noTiltScan,
+    				measurement,
+    				false, // boolean parallelMove,
+    				true, // boolean noQualB,   // do not re-claculate testQualB 
+    				noMotors); // boolean noAdjust) // do not calculate correction
     		if (ZTM!=null) {
     			for (int i=0;i<result.length;i++) result[i]+=ZTM[i];
     			num++;
@@ -5147,7 +5166,10 @@ public boolean LevenbergMarquardt(
     public double [] adjustLMA ( // result relative to optimal
     		boolean noTiltScan,
     		FocusingFieldMeasurement measurement,
-    		boolean parallelMove){
+    		boolean parallelMove,
+    		boolean noQualB,   // do not re-claculate testQualB 
+    		boolean noAdjust){ // do not calculate correction
+    	if (!noQualB) {
     		if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode);
     		testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
     		if (debugLevel>0) {
@@ -5155,6 +5177,7 @@ public boolean LevenbergMarquardt(
     			System.out.println("Optimal Tx="+this.qualBOptimizationResults[1]);
     			System.out.println("Optimal Ty="+this.qualBOptimizationResults[2]);
     		}
+    	}
     	if (!testMeasurement(
     			measurement,    				
 				zMin, //+best_qb_corr[0],
@@ -5166,23 +5189,16 @@ public boolean LevenbergMarquardt(
 			if (debugLevel>0) System.out.println("adjustLMA() failed");
     		return null;
     	}
-    	double [] result=new double [6];
-    	
-//        double [] best_qb_corr= fieldFitting.getBestQualB(
-//                k_red,
-//                k_blue,
-//                true);
+    	double [] result=new double [noAdjust?3:6];
         
         double [] zTilts=getCenterZTxTy(measurement);
         result[0]=zTilts[0]-this.qualBOptimizationResults[0]; //best_qb_corr[0];
         result[1]=zTilts[1]-this.qualBOptimizationResults[1];
         result[2]=zTilts[2]-this.qualBOptimizationResults[2];
+        if (!noAdjust) {
         	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);
-//        }
-        	
         	if (this.debugLevel>0){
         		System.out.println("Current linearized motor positions, center="+(0.25*zm[0]+0.25*zm[1]+0.5*zm[2]));
         		for (int i=0;i<zm.length;i++) {
@@ -5214,6 +5230,7 @@ public boolean LevenbergMarquardt(
         		result[4]=Double.NaN;
         		result[5]=Double.NaN;
         	}
+        }
         return result;
     }
     
@@ -5310,7 +5327,7 @@ public boolean LevenbergMarquardt(
     		zTxTy[0]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.z0);
     		zTxTy[1]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.tx);
     		zTxTy[2]=fieldFitting.mechanicalFocusingModel.getValue(MECH_PAR.ty);
-    		if (debugLevel>0) System.out.println("testMeasurement(), run "+n+" (z="+zTxTy[0]+" tx="+zTxTy[1]+" ty="+zTxTy[2]+")");
+    		if (debugLevel>1) System.out.println("testMeasurement(), run "+n+" (z="+zTxTy[0]+" tx="+zTxTy[1]+" ty="+zTxTy[2]+")");
     		boolean [] was2PrevEnable=(wasPrevEnable==null)?null:wasPrevEnable.clone();
     		wasPrevEnable=(prevEnable==null)?null:prevEnable.clone();
     		this.lambda=this.adjustmentInitialLambda;
@@ -5340,8 +5357,8 @@ public boolean LevenbergMarquardt(
     				break;
     			}
     			if (!changedEnable) {
-    				if (debugLevel>0) System.out.println("No filter cnange, finished in "+(n+1)+" step"+((n==0)?"":"s"));
-    				if (debugLevel>0) {
+    				if (debugLevel>1) System.out.println("No filter cnange, finished in "+(n+1)+" step"+((n==0)?"":"s"));
+    				if (debugLevel>1) {
     					System.out.println("=== Absolute shift/tilt from the measuremet ===");
     					for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
     						if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
@@ -9609,7 +9626,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx ->  ar[1], ar[2], ar[3],  ar[4]
 
         	String msg="QualB="+this.currentQualB+" ("+this.firstQualB+") "+
         			" at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.qStartTime),3);
-        	if (debugLevel>0) System.out.println("qStepLevenbergMarquardtAction() "+msg);
+        	if (debugLevel>1) System.out.println("qStepLevenbergMarquardtAction() "+msg);
         	//    	if (this.updateStatus) IJ.showStatus(msg);
         	if (updateStatus){
         		IJ.showStatus("Done: Step #"+this.iterationStepNumber+

src/main/java/LensAdjustment.java

@@ -195,6 +195,7 @@ public class LensAdjustment {
     	public String gridGeometryFile="";
     	public String initialCalibrationFile="";
     	public String focusingHistoryFile="";
+    	public boolean useLMAMetrics=true; // measure/report focal distance and tilts using lens model/LMA (when available)
     	public String strategyFile="";
     	public String resultsSuperDirectory=""; // directory with subdirectories named as serial numbers to stro results
     	public int EEPROM_channel=1; // EEPROM channel to read serial number from
@@ -430,6 +431,7 @@ public class LensAdjustment {
     	    	String strategyFile,
     	    	String resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results
     	    	String focusingHistoryFile,
+    	    	boolean useLMAMetrics, // measure/report focal distance and tilts using lens model/LMA (when available)
     	    	int EEPROM_channel, // EEPROM channel to read serial number from
     	    	boolean saveResults, // save focusing results
     	    	boolean showResults, // show focusing (includingh intermediate) results
@@ -577,6 +579,7 @@ public class LensAdjustment {
     		this.strategyFile=strategyFile;
     		this.resultsSuperDirectory=resultsSuperDirectory; // directory with subdirectories named as serial numbers to stro results
     		this.focusingHistoryFile=focusingHistoryFile;
+    		this.useLMAMetrics=useLMAMetrics; // measure/report focal distance and tilts using lens model/LMA (when available)
     		this.EEPROM_channel=EEPROM_channel; // EEPROM channel to read serial number from
     		this.saveResults=saveResults; // save focusing results
     		this.showResults=showResults; // show focusing (includingh intermediate) results
@@ -725,6 +728,7 @@ public class LensAdjustment {
     	    		this.strategyFile,
     	    		this.resultsSuperDirectory, // directory with subdirectories named as serial numbers to stro results
     	    		this.focusingHistoryFile,
+    	    		this.useLMAMetrics, // measure/report focal distance and tilts using lens model/LMA (when available)
     	    		this.EEPROM_channel,// EEPROM channel to read serial number from
     	    		this.saveResults, // save focusing results
     	    		this.showResults, // show focusing (includingh intermediate) results
@@ -871,6 +875,7 @@ public class LensAdjustment {
 			properties.setProperty(prefix+"strategyFile",this.strategyFile+"");
 			properties.setProperty(prefix+"resultsSuperDirectory",this.resultsSuperDirectory+"");
 			properties.setProperty(prefix+"focusingHistoryFile",this.focusingHistoryFile+"");
+			properties.setProperty(prefix+"useLMAMetrics",this.useLMAMetrics+"");
 			properties.setProperty(prefix+"serialNumber",this.serialNumber+"");
 			if (!Double.isNaN(this.sensorTemperature))properties.setProperty(prefix+"sensorTemperature",this.sensorTemperature+"");
 			if (!Double.isNaN(this.result_lastKT))properties.setProperty(prefix+"result_lastKT",this.result_lastKT+"");
@@ -1030,6 +1035,9 @@ public class LensAdjustment {
 			if (properties.getProperty(prefix+"focusingHistoryFile")!=null)
 				this.focusingHistoryFile=properties.getProperty(prefix+"focusingHistoryFile");
 
+			if (properties.getProperty(prefix+"useLMAMetrics")!=null)
+				this.useLMAMetrics=Boolean.parseBoolean(properties.getProperty(prefix+"useLMAMetrics"));
+			
 			if (properties.getProperty(prefix+"serialNumber")!=null)
 				this.serialNumber=properties.getProperty(prefix+"serialNumber");
 			//	this.serialNumber is only written, but never read from the configuration file (only from devivce)
@@ -1441,7 +1449,8 @@ public class LensAdjustment {
 			gd.addStringField  ("Initial camera intrinsic/extrinsic parametres file", this.initialCalibrationFile,40);
 			gd.addStringField  ("Levenberg-Marquardt algorithm strategy file",        this.strategyFile,40);
 			gd.addStringField  ("Focusing results superdirectory (individual will be named by serial numbers)", this.resultsSuperDirectory,40);
-			gd.addStringField  ("Measurement history (acquired during \"Scan Calib LMA\" file", this.focusingHistoryFile,80);
+			gd.addStringField  ("Measurement history (acquired during \"Scan Calib LMA\") file", this.focusingHistoryFile,80);
+			gd.addCheckbox     ("Use lens aberration model (if available) for focal distance and tilts", this.useLMAMetrics);
 			gd.addNumericField("EEPROM channel to read sensor serial number from",    this.EEPROM_channel, 0,4,"");
 			gd.addCheckbox    ("Save SFE focusing results (including intermediate) ", this.saveResults);
 			gd.addCheckbox    ("Show SFE focusing results (including intermediate) ", this.showResults);
@@ -1618,6 +1627,8 @@ public class LensAdjustment {
 			this.strategyFile=               gd.getNextString();
     		this.resultsSuperDirectory=      gd.getNextString();
     		this.focusingHistoryFile=        gd.getNextString();
+			this.useLMAMetrics =             gd.getNextBoolean();
+
     		this.EEPROM_channel=       (int) gd.getNextNumber();
 			this.saveResults=                gd.getNextBoolean();
 			this.showResults=                gd.getNextBoolean();