Added initial z0 estimate, switched squared parameters to exp() (123e14a3) · Commits · Elphel / imagej-elphel

src/main/java/FocusingField.java

+96 −66

Original line number	Diff line number	Diff line
		@@ -96,7 +96,7 @@ public class FocusingField {
		private boolean [] rslt_show_chn;

		// not saved/restored

		private double [] z0_estimates=null; // initial estimates for z0 from the lowest value on data
		private double lambdaStepUp; // multiply lambda by this if result is worse
		private double lambdaStepDown; // multiply lambda by this if result is better
		private double thresholdFinish; // (copied from series) stop iterations if 2 last steps had less improvement (but not worsening )
		@@ -170,6 +170,7 @@ public class FocusingField {


		public void setDefaults(){
		z0_estimates=null;
		sagittalMaster=false; // center data is the same, when true sagittal fitting only may change r=0 coefficients,
		parallelOnly = true; // only process measurements for parallel moves
		filterInput = true;
		@@ -666,7 +667,12 @@ private boolean [] filterConcave(
		int numFilteredInsufficient = 0;
		int numFiltered = 0;
		int [][] numPoints=new int [getNumChannels()][getNumSamples()];
		for (int chn=0;chn<numPoints.length;chn++) for (int sample=0;sample<numPoints[chn].length;sample++) numPoints[chn][sample]=0;
		double [][][] z0EstData=new double[getNumChannels()][getNumSamples()][2];
		for (int chn=0;chn<numPoints.length;chn++) for (int sample=0;sample<numPoints[chn].length;sample++) {
		numPoints[chn][sample]=0;
		z0EstData[chn][sample][0]=0.0;
		z0EstData[chn][sample][1]=0.0;
		}
		for (int index=0;index<dataVector.length;index++) if ((index>=enable_in.length) \|\|enable_in[index]){
		numPoints[dataVector[index].channel][dataVector[index].sampleIndex]++;
		}
		@@ -811,13 +817,30 @@ private boolean [] filterConcave(
		", slope="+ IJ.d2s(100*point_slope[i],3)+ ", concave="+(nonConcave[i]?0.0:1.0));
		}
		}
		// contribute to z0 calculation
		for (int i=0;i<thisIndices.length;i++) if (!nonConcave[i]){
		z0EstData[chn][sample][1]+=dataWeights[thisIndices[i]];
		}
		z0EstData[chn][sample][0]=point_z[minIndex];
		}
		}
		if (debugLevel>0) System.out.println("filterConcave(): removed for too few points "+numFilteredInsufficient+" samples");
		if (debugLevel>0) System.out.println("filterConcave(): removed for non-concave "+numFiltered+" samples");
		return enable_out;

		// for (int chn=0;chn<numPoints.length;chn++) for (int sample=0;sample<numPoints[chn].length;sample++){
		z0_estimates=new double[getNumChannels()];
		for (int chn=0;chn<z0_estimates.length;chn++){
		double z=0;
		double w=0;
		for (int sample=0;sample<numPoints[chn].length;sample++){
		z+=z0EstData[chn][sample][0]*z0EstData[chn][sample][1];
		w+=z0EstData[chn][sample][1];
		}
		z0_estimates[chn]= (w>0.0)?z/w:Double.NaN;
		}

		return enable_out;
		}

		private boolean [] filterTooFar(double ratio,boolean [] enable_in){
		if (enable_in==null) {
		@@ -2707,7 +2730,7 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
		fieldFitting.initSampleCorrVector(
		flattenSampleCoord(), //double [][] sampleCoordinates,
		getSeriesWeights()); //double [][] sampleSeriesWeights);

		fieldFitting.setEstimatedZ0( z0_estimates, false); // boolean force)

		this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
		if (debugDerivativesFxDxDy){
		@@ -3774,6 +3797,18 @@ if ((chn==3) && (sampleIndex==23)){
		}
		}

		public void setEstimatedZ0(
		double [] z0,
		boolean force){
		if ((z0==null)\|\| (curvatureModel==null)) return; // no estimation available
		for (int chn=0;chn<curvatureModel.length;chn++){
		if (!Double.isNaN(z0[chn]) && (!curvatureModel[chn].z0IsValid() \|\| force)){
		curvatureModel[chn].set_z0(z0[chn]);
		if (debugLevel>1) System.out.println("Setting initial (estimated) best focal position for channel "+chn+" = "+z0[chn]);
		}
		}
		}

		/**
		* create matrix of weights of the other parameters influence
		* @param sampleCoordinates [sample number]{x,y} - flattened array of sample coordinates
		@@ -3828,29 +3863,6 @@ if ((chn==3) && (sampleIndex==23)){
		}
		}
		getCorrVector();

		/*
		sampleCorrChnParIndex=new int [sampleCorrSelect.length][];
		int numPars=0;
		for (int nChn=0; nChn< sampleCorrCrossWeights.length;nChn++) {
		if (sampleCorrCrossWeights[nChn]!=null){
		sampleCorrChnParIndex[nChn]=new int [sampleCorrCrossWeights[nChn].length];
		for (int nPar=0;nPar< sampleCorrCrossWeights[nChn].length;nPar++) {
		if (sampleCorrCrossWeights[nChn][nPar]!=null){
		sampleCorrChnParIndex[nChn][nPar]=numPars; // pointer to the first sample
		numPars+=sampleCorrCrossWeights[nChn][nPar].length;
		} else {
		sampleCorrChnParIndex[nChn][nPar]=-1;
		}
		}
		} else {
		sampleCorrChnParIndex[nChn]=null;
		}
		}
		// currently all correction parameters are initialized as zeros.
		getCorrVector();
		if (debugLevel>1) System.out.println("was resetting sampleCorrVector here");
		*/
		}


		@@ -3888,15 +3900,6 @@ if ((chn==3) && (sampleIndex==23)){
		return sampleCoordinates;
		}
		public double [] getCorrPar(int chn, int sampleIndex){
		/* if ((sampleCorrChnParIndex==null) \|\| (sampleCorrChnParIndex[chn]==null)) return null;
		double [] corr =new double [sampleCorrChnParIndex[chn].length];
		for (int i=0;i<corr.length;i++){
		if (sampleCorrChnParIndex[chn][i]<0) corr[i]=0.0;
		else corr[i]=sampleCorrVector[sampleCorrChnParIndex[chn][i]+sampleIndex];
		}
		*/
		// System.out.println("used sampleCorrVector here, now correctionParameters");

		if (correctionParameters[chn]==null) return null;
		double [] corr =new double [correctionParameters[chn].length];
		for (int i=0;i<corr.length;i++){
		@@ -4859,8 +4862,8 @@ if ((chn==3) && (sampleIndex==23)){
		}

		public class CurvatureModel{
		private double dflt_na=0.15; // um/um
		private double dflt_r0=4.0; //3.3; // um (1.5 pix)
		private double dflt_na=Math.log(0.15); // um/um
		private double dflt_r0=Math.log(4.0); //3.3; // um (1.5 pix)
		private double [][] modelParams=null;
		public static final int dflt_distanceParametersNumber=5;
		public static final int dflt_radialParametersNumber=4;
		@@ -4934,7 +4937,16 @@ if ((chn==3) && (sampleIndex==23)){
		}
		this.modelParams[1][0]=dflt_na;
		this.modelParams[2][0]=dflt_r0;
		this.modelParams[0][0]=Double.NaN;
		}
		public boolean z0IsValid(){
		return !Double.isNaN(this.modelParams[0][0]);
		}

		public void set_z0(double z0){
		this.modelParams[0][0]=z0;
		}

		public double [] getCenterVector(){
		double [] vector=new double [this.modelParams.length];
		for (int i=0;i<this.modelParams.length;i++){
		@@ -5014,12 +5026,24 @@ modified parameters, r0 - PSF FWHM at z=0, k (instead of a0), so that old r0 now
		r0exp(-k), old a0= r0(1-exp(-k)).

		f=sqrt((a(zin-z0))^2 + (r0(exp(-k))^2)+r0(1-exp(-k))+ a1(zin-z0)+...aN*(zin-z0)^N

		z0 - ar[0]
		a - ar[1]
		r0 - ar[2]
		k - ar[3]
		ar1 - ar[4]

		modified to avoid zero-crossing for a and r0:
		a=exp(ln_a)
		r0=exp(ln_r0)

		z0 - ar[0]
		ln_a - ar[1]
		ln_r0 - ar[2]
		k - ar[3]
		ar1 - ar[4]


		*/
		double r=Double.isNaN(pY)?pX:Math.sqrt((pX-pX0)(pX-pX0)+(pY-pY0)(pY-pY0))*PIXEL_SIZE; // in mm
		// double r2=r*r;
		@@ -5035,20 +5059,19 @@ ar1 - ar[4]
		ar[i]+=this.modelParams[i][j]*rp;
		}
		}
		double exp_a=Math.exp(ar[1]);
		double exp_r=Math.exp(ar[2]);
		double z=z_in-ar[0];
		double exp=Math.exp(-ar[3]);
		double reff=ar[2]*exp;
		// double sqrt=Math.sqrt((ar[1]z)(ar[1]z) + ar[2]ar[2]);
		double sqrt=Math.sqrt((ar[1]z)(ar[1]z) + reffreff);

		double f=sqrt+ar[2]*(1-exp);
		double exp_k=Math.exp(-ar[3]);
		// double reff=ar[2]*exp_k;
		double reff=exp_r*exp_k;
		// double sqrt=Math.sqrt((ar[1]z)(ar[1]z) + reffreff);
		double sqrt=Math.sqrt((exp_az)(exp_az) + reffreff);

		// double f=sqrt+ar[2]*(1-exp_k);
		double f=sqrt+exp_r*(1-exp_k);
		double zp=1.0;
		/*
		for (int i=3;i<ar.length;i++){
		f+=ar[i]*zp;
		zp*=z;
		}
		*/

		for (int i=4;i<ar.length;i++){
		zp*=z;
		f+=ar[i]*zp;
		@@ -5057,29 +5080,35 @@ ar1 - ar[4]
		if (deriv==null) return f; // only value, no derivatives
		double [] df_da=new double[this.modelParams.length]; // last element - derivative for dz
		// derivative for z0 (shift) - ar[0]
		df_da[0]=-1.0/sqrtar[1]ar[1]*z;
		// df_da[0]=-1.0/sqrtar[1]ar[1]*z;

		df_da[0]=-1.0/sqrtexp_aexp_a*z;

		zp=1.0;
		for (int i=4;i<this.modelParams.length;i++){
		df_da[0]-=ar[i](i-3)zp; // ar[i] calculated coefficients for current radius
		zp*=z;
		}
		// derivative for a (related to numeric aperture) - ar[1]
		df_da[1]=1.0/sqrtar[1]z*z;
		// df_da[1]=1.0/sqrtar[1]z*z;
		df_da[1]=1.0/sqrtexp_azz exp_a; // d(f)/d(exp_a) *exp_a


		// derivative for a (related to lowest PSF radius) - ar[2]
		// df_da[2]=1.0/sqrt*ar[2];
		df_da[2]=1.0/sqrtreffexp + (1-exp); // * exp(-k)
		// df_da[2]=1.0/sqrtreffexp_k + (1-exp_k); // * exp(-k)
		df_da[2]=(1.0/sqrtreffexp_k + (1-exp_k)) * exp_r; // d(f)/d(exp_r) *exp_r




		// derivative for k (ar[3]

		df_da[3]=1.0/sqrtreffar[2]exp(-1) + ar[2]*exp;
		// df_da[3]=1.0/sqrtreffar[2]exp_k(-1) + ar[2]*exp_k;
		df_da[3]=1.0/sqrtreffexp_rexp_k(-1) + exp_r*exp_k;

		// derivatives for rest (polynomial) coefficients
		zp=1.0;
		/*
		for (int i=3;i<this.modelParams.length;i++){
		df_da[i]=zp;
		zp*=z;
		}
		*/

		for (int i=4;i<this.modelParams.length;i++){
		zp*=z;
		df_da[i]=zp;
		@@ -5089,7 +5118,6 @@ ar1 - ar[4]
		double [] dar= new double [this.modelParams[0].length];
		dar[0]=1;
		for (int j=1;j<dar.length;j++){
		// dar[j]=dar[j-1]*r2;
		dar[j]=dar[j-1]*r;
		if (j==1) dar[j]*=r; // 0,2,3,4,5...
		}
		@@ -5120,14 +5148,16 @@ ar1 - ar[4]
		}
		public String getZName(int i){
		if (i==0) return "z0";
		if (i==1) return "na";
		if (i==2) return "r0";
		if (i==1) return "ln(na)";
		if (i==2) return "ln(r0)";
		if (i==3) return "ln(k)";
		else return "az_"+(i-3);
		}
		public String getZDescription(int i){
		if (i==0) return "Focal shift";
		if (i==1) return "Defocus/focus shift (~NA)";
		if (i==2) return "Best PSF radius";
		if (i==1) return "Defocus/focus shift (~NA), ln()";
		if (i==2) return "Best PSF radius, ln()";
		if (i==3) return "cross shift, ln()";
		else return "Polynomial coefficient for z^"+(i-3);
		}

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