minor bug fixes (fd3a84bd) · Commits · Elphel / imagej-elphel

src/main/java/FocusingField.java

+66 −38

Original line number	Diff line number	Diff line
		@@ -96,6 +96,7 @@ public class FocusingField {
		private double rslt_scan_above;
		private double rslt_scan_step;
		private boolean rslt_mtf50_mode;
		private boolean rslt_solve; // find z for minimum of f, if false - use parameter z0
		private boolean [] rslt_show_chn;

		// not saved/restored
		@@ -219,6 +220,7 @@ public class FocusingField {
		rslt_scan_above= 10.0;
		rslt_scan_step= 5.0;
		rslt_mtf50_mode= true;
		rslt_solve = false;
		boolean [] rslt_show_chnDflt={true,true,true,true,true,true};
		rslt_show_chn=rslt_show_chnDflt.clone();
		// not saved/restored
		@@ -317,6 +319,7 @@ public class FocusingField {
		properties.setProperty(prefix+"rslt_scan_above",rslt_scan_above+"");
		properties.setProperty(prefix+"rslt_scan_step",rslt_scan_step+"");
		properties.setProperty(prefix+"rslt_mtf50_mode",rslt_mtf50_mode+"");
		properties.setProperty(prefix+"rslt_solve",rslt_solve+"");
		for (int chn=0; chn<rslt_show_chn.length; chn++) properties.setProperty(prefix+"rslt_show_chn_"+chn,rslt_show_chn[chn]+"");
		}

		@@ -422,6 +425,8 @@ public class FocusingField {
		rslt_scan_step=Double.parseDouble(properties.getProperty(prefix+"rslt_scan_step"));
		if (properties.getProperty(prefix+"rslt_mtf50_mode")!=null)
		rslt_mtf50_mode=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_mtf50_mode"));
		if (properties.getProperty(prefix+"rslt_solve")!=null)
		rslt_solve=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_solve"));
		for (int chn=0; chn<rslt_show_chn.length; chn++) if (properties.getProperty(prefix+"rslt_show_chn_"+chn)!=null)
		rslt_show_chn[chn]=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_show_chn_"+chn));
		}
		@@ -618,6 +623,7 @@ public boolean configureDataVector(String title, boolean forcenew, boolean enabl
		getProperties(propertiesPrefix,savedProperties);
		}
		}
		fieldFitting.setCenterXY(currentPX0,currentPY0);
		if (setupMasks) {
		if (!fieldFitting.maskSetDialog("Setup parameter masks")) return false;
		}
		@@ -2402,11 +2408,11 @@ public void listCombinedResults(){
		// private boolean rslt_mtf50_mode= true;
		// public double fwhm_to_mtf50=500.0; // put actual number

		double [] center_z=fieldFitting.getZCenters(false);
		double [] center_z=fieldFitting.getZCenters(false); // do not solve, use z0 coefficient
		double [] centerFWHM={
		fieldFitting.getCalcValuesForZ(center_z[0],0.0)[1],
		fieldFitting.getCalcValuesForZ(center_z[1],0.0)[3],
		fieldFitting.getCalcValuesForZ(center_z[2],0.0)[5]
		fieldFitting.getCalcValuesForZ(center_z[0],0.0,null)[1],
		fieldFitting.getCalcValuesForZ(center_z[1],0.0,null)[3],
		fieldFitting.getCalcValuesForZ(center_z[2],0.0,null)[5]
		};
		double [] best_qb_axial= fieldFitting.getBestQualB(
		k_red,
		@@ -2438,6 +2444,8 @@ public void listCombinedResults(){
		gd.addCheckbox("Show constant-z sections (per-sample adjusted)", this.rslt_show_f_individual);
		gd.addNumericField("Ring averaging radial sigma", this.rslt_show_smooth_sigma, 3,5,"mm");
		gd.addCheckbox("Show mtf50 (false - PSF FWHM)", this.rslt_mtf50_mode);
		gd.addCheckbox("Find z for minimum, unchecked - use parameter", this.rslt_solve);

		gd.addCheckbox("Show focal distance relative to best composite focus (false - to center green )", this.z_relative);

		gd.addMessage("Multiple section setup:");
		@@ -2459,8 +2467,8 @@ public void listCombinedResults(){
		this.rslt_show_f_smooth= gd.getNextBoolean();
		this.rslt_show_f_individual= gd.getNextBoolean();
		this.rslt_show_smooth_sigma= gd.getNextNumber();

		this.rslt_mtf50_mode= gd.getNextBoolean();
		this.rslt_solve=gd.getNextBoolean();
		this.z_relative= gd.getNextBoolean();
		this.rslt_scan_below= gd.getNextNumber();
		this.rslt_scan_above= gd.getNextNumber();
		@@ -2481,7 +2489,8 @@ public void listCombinedResults(){
		(z_relative?best_qb_corr[0]:center_z[1])+rslt_scan_below, // double scan_below,
		(z_relative?best_qb_corr[0]:center_z[1])+rslt_scan_above, //double scan_above,
		rslt_scan_step, //double scan_step,
		rslt_mtf50_mode); //boolean freq_mode)
		rslt_mtf50_mode, //boolean freq_mode)
		rslt_solve); // currently if not using z^(>=2) no numeric solution is required - z0 is the minimum
		}

		public double [][] filterListSamples(
		@@ -2542,7 +2551,9 @@ public void listCombinedResults(
		double scan_below,
		double scan_above,
		double scan_step,
		boolean freq_mode){
		boolean freq_mode,
		boolean solveZ){ // currently if not using z^(>=2) no numeric solution is required - z0 is the minimum

		String [] chnNames={"RS","RT","GS","GT","BS","BT"};
		// Calculate weights of each channel/sample
		double [][] sampleWeights=new double[getNumChannels()][getNumSamples()];
		@@ -2602,7 +2613,7 @@ public void listCombinedResults(
		for (double z=scan_below;z<=scan_above;z+=scan_step){
		if (show_f_axial){
		double [][] f=fieldFitting.getCalcValuesForZ(z, false,true);
		double [] f0=fieldFitting.getCalcValuesForZ(z, 0.0);
		double [] f0=fieldFitting.getCalcValuesForZ(z, 0.0,null);
		f_values[sect][0]=new double [f.length][];
		for (int chn=0;chn<f.length;chn++){
		if (f[chn]!=null){
		@@ -2652,8 +2663,8 @@ public void listCombinedResults(
		}
		double [][][] z_values=new double [3][][];
		if (show_z_axial){
		double [][] zai=fieldFitting.getCalcZ(false,true);
		double [] zai0=fieldFitting.getCalcZ(0.0);
		double [][] zai=fieldFitting.getCalcZ(false,true,solveZ);
		double [] zai0=fieldFitting.getCalcZ(0.0,solveZ);
		z_values[0]=new double [zai.length][];
		for (int chn=0;chn<zai.length;chn++){
		if (zai[chn]!=null){
		@@ -2667,7 +2678,7 @@ public void listCombinedResults(
		}
		} else z_values[0] = null;
		if (show_z_individual){
		double [][] zai=fieldFitting.getCalcZ(true,true);
		double [][] zai=fieldFitting.getCalcZ(true,true,solveZ);
		z_values[1]=new double [zai.length][];
		for (int chn=0;chn<zai.length;chn++){
		if (zai[chn]!=null){
		@@ -2681,7 +2692,7 @@ public void listCombinedResults(
		}
		} else z_values[1] = null;
		if (show_f_smooth){
		double [][] zai=fieldFitting.getCalcZ(true,true);
		double [][] zai=fieldFitting.getCalcZ(true,true,solveZ);
		z_values[2]=new double [zai.length][];
		for (int chn=0;chn<zai.length;chn+=2){
		double [][] smooth=filterListSamples(
		@@ -2757,11 +2768,11 @@ public void listCombinedResults(

		public void listScanQB(){

		double [] center_z=fieldFitting.getZCenters(false);
		double [] center_z=fieldFitting.getZCenters(false); // do not solve, use z0 coefficient
		double [] centerFWHM={
		fieldFitting.getCalcValuesForZ(center_z[0],0.0)[1],
		fieldFitting.getCalcValuesForZ(center_z[1],0.0)[3],
		fieldFitting.getCalcValuesForZ(center_z[2],0.0)[5]
		fieldFitting.getCalcValuesForZ(center_z[0],0.0,null)[1],
		fieldFitting.getCalcValuesForZ(center_z[1],0.0,null)[3],
		fieldFitting.getCalcValuesForZ(center_z[2],0.0,null)[5]
		};
		double [] best_qb_axial= fieldFitting.getBestQualB(
		k_red,
		@@ -2853,11 +2864,11 @@ public void listScanQB(
		// }

		// Add result to the bottom of the file
		double [] center_z=fieldFitting.getZCenters(false);
		double [] center_z=fieldFitting.getZCenters(false); // z0 coefficient, do not find minimum
		double [] centerFWHM={
		fieldFitting.getCalcValuesForZ(center_z[0],0.0)[1],
		fieldFitting.getCalcValuesForZ(center_z[1],0.0)[3],
		fieldFitting.getCalcValuesForZ(center_z[2],0.0)[5]
		fieldFitting.getCalcValuesForZ(center_z[0],0.0,null)[1],
		fieldFitting.getCalcValuesForZ(center_z[1],0.0,null)[3],
		fieldFitting.getCalcValuesForZ(center_z[2],0.0,null)[5]
		};
		// double [] best_qb_axial= fieldFitting.getBestQualB(
		// k_red,
		@@ -3592,12 +3603,12 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		titles);

		}
		public double [] getCalcValuesForZ(double z, double r){
		public double [] getCalcValuesForZ(double z, double r, double [] corrPars){
		double [] result=new double [6];
		for (int chn=0;chn<result.length;chn++) {
		if (curvatureModel[chn]!=null){
		result[chn]=curvatureModel[chn].getFdF(
		null,
		corrPars,
		r, // in mm,
		Double.NaN, // py,
		z, //mot_z,
		@@ -3642,12 +3653,14 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		return result;
		}

		public double [] getCalcZ(double r){
		public double [] getCalcZ(double r,
		boolean solve // currently if not using z^(>=2) no numeric solution is required - z0 is the minimum
		){
		double [] result=new double [6];
		for (int chn=0;chn<result.length;chn++) {
		if (curvatureModel[chn]!=null){
		// result[chn]=curvatureModel[chn].getAr(r, null)[0];
		result[chn]=findBestZ(chn, -1, false);
		result[chn]=findBestZ(chn, -1, false,solve);
		} else {
		result[chn]=Double.NaN;
		}
		@@ -3657,11 +3670,14 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		public double findBestZ(
		int channel,
		int sampleIndex, // -1 for center
		boolean corrected){
		boolean corrected,
		boolean solve // currently if not using z^(>=2) no numeric solution is required - z0 is the minimum
		){
		return findBestZ(
		channel,
		sampleIndex, // -1 for center
		corrected, //
		solve, // currently if not using z^(>=2) no numeric solution is required - z0 is the minimum
		1.0, // double iniStep,
		0.0001); //double precision)
		}
		@@ -3670,16 +3686,18 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		int channel,
		int sampleIndex, // -1 for center
		boolean corrected, //
		boolean solve, // currently if not using z^(>=2) no numeric solution is required - z0 is the minimum
		double iniStep,
		double precision){
		int maxSteps=100;
		double [] corrPars=corrected?getCorrPar(channel,sampleIndex):null;
		double r=(sampleIndex>=0)?getSampleRadius(sampleIndex):0.0;
		double z0=curvatureModel[channel].getAr( r, corrPars)[0];
		if (!solve) return z0;
		if (Double.isNaN(z0)) return z0;
		double f0=getCalcValuesForZ(z0, r)[channel];
		double f0=getCalcValuesForZ(z0, r,corrPars)[channel];
		double z1=z0+iniStep;
		double f1=getCalcValuesForZ(z1,r)[channel];
		double f1=getCalcValuesForZ(z1,r,corrPars)[channel];
		double dir = (f1<f0)?1.0:-1.0;
		double z_prev,f_prev;
		if (dir>0) {
		@@ -3694,7 +3712,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		int step;
		for (step=0;step<maxSteps;step++) {
		z1=z0+dir*iniStep;
		f1=getCalcValuesForZ(z1,r)[channel];
		f1=getCalcValuesForZ(z1,r,corrPars)[channel];
		if (f1>f0) break;
		z_prev=z0;
		f_prev=f0;
		@@ -3716,7 +3734,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		}
		z0=(z_prev+z1)/2;
		// f0=getCalcValuesForZ(z1,r)[channel]; // ????
		f0=getCalcValuesForZ(z0,r)[channel];
		f0=getCalcValuesForZ(z0,r,corrPars)[channel];
		if (Math.abs(z0-z_prev)<precision) break;
		}
		return z0;
		@@ -3728,7 +3746,11 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		* @param allChannels calculate for all (even disabled) channels, false - only for currently selected
		* @return outer dimension - number of channel, inner - number of sample (use getSampleRadiuses for radius of each)
		*/
		public double [][] getCalcZ(boolean corrected, boolean allChannels){
		public double [][] getCalcZ(
		boolean corrected,
		boolean allChannels,
		boolean solve // currently if not using z^(>=2) no numeric solution is required - z0 is the minimum
		){
		double [] sampleCorrRadius=getSampleRadiuses();
		int numSamples=sampleCorrRadius.length;
		boolean [][] goodSamples=new boolean[getNumChannels()][getNumSamples()];
		@@ -3753,7 +3775,8 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		result[chn][sampleIndex]=findBestZ(
		chn, // int channel,
		sampleIndex, // int sampleIndex,
		corrected); //boolean corrected,
		corrected, //boolean corrected,
		solve);
		} else {
		result[chn][sampleIndex]=Double.NaN;
		}
		@@ -3777,9 +3800,9 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		curvatureModel[5].getCenterVector()[0]}; // Blue, Tangential
		if (solve) {
		double [] result_1 = {
		findBestZ(1, -1, false),
		findBestZ(3, -1, false),
		findBestZ(5, -1, false),
		findBestZ(1, -1, false,true),
		findBestZ(3, -1, false,true),
		findBestZ(5, -1, false,true),
		};
		return solve?result_1:result;
		}
		@@ -3923,6 +3946,10 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		public double[] getCenterXY(){
		return pXY;
		}
		public void setCenterXY(double px, double py){
		pXY[0]=px;
		pXY[1]=py;
		}
		public void setDefaultSampleCorr(){
		// int numPars= getNumCurvars()[0]; // number of Z parameters ( [1] - numbnr of radial parameters).
		for (int n=0;n<channelDescriptions.length;n++){
		@@ -4465,10 +4492,11 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		gd.addMessage("===== Aberrations center =====");
		String [] centerDescriptions={"Aberrations center X","Aberrations center Y"};
		for (int i=0;i<2;i++){
		double distXY=(i==0)?pX0_distortions:pY0_distortions;
		if (centerSelect[i] ) {
		gd.addNumericField(centerDescriptions[i],pXY[i],5,10,"pix");
		gd.addNumericField(centerDescriptions[i],pXY[i],5,10,"pix ("+IJ.d2s(distXY,1)+")");
		} else if (showDisabled){
		gd.addNumericField("(disabled) "+centerDescriptions[i],pXY[i],5,10,"pix");
		gd.addNumericField("(disabled) "+centerDescriptions[i],pXY[i],5,10,"pix ("+IJ.d2s(distXY,1)+")");
		}
		}

		@@ -5467,7 +5495,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
		//z_corr: kx,r_eff,a - ar[1], ar[4], ar[2], ar[3]
		double sqr_azr=Math.sqrt(exp_a2*z_corr2+reff2);

		double dfcorr_da=exp_a*z_corr2/sqr_azr;
		// double dfcorr_da=exp_a*z_corr2/sqr_azr;
		double dfcorr_dreff=reff/sqr_azr-1;
		double dfcorr_dkx=-z_corr;
		// dfcorr_dar1==0

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