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Commit ee11a47a authored by Andrey Filippov's avatar Andrey Filippov
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more bug fixes

parent 123e14a3
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Showing with 405 additions and 75 deletions
src/main/java/FocusingField.java
View file @ ee11a47a
......@@ -86,9 +86,12 @@ public class FocusingField {
private boolean qb_invert;
private boolean z_relative; // focal distance relative to center greeen
private boolean rslt_show_z_axial;
private boolean rslt_show_z_smooth;
private boolean rslt_show_z_individual;
private boolean rslt_show_f_axial;
private boolean rslt_show_f_smooth;
private boolean rslt_show_f_individual;
private double rslt_show_smooth_sigma;
private double rslt_scan_below;
private double rslt_scan_above;
private double rslt_scan_step;
......@@ -195,7 +198,7 @@ public class FocusingField {
useMinMeas= true;
useMaxMeas= true;
useThresholdMax=true;
weightMode=1; // 0; // 0 - same weight, 1 - linear threshold difference, 2 - quadratic thershold difference
weightMode=2; // 1; // 0 - same weight, 1 - linear threshold difference, >1 - power of PSF radius
weightRadius=0.0; //2.0; // Gaussian sigma in mm
k_red=0.7;
k_blue=0.4;
......@@ -204,11 +207,14 @@ public class FocusingField {
qb_scan_step= 0.5; // um
qb_use_corrected=true;
qb_invert=true;
z_relative=true; // focal distance relative to center greeen
z_relative=true; // focal distance relative to best overall (false - center green )
rslt_show_z_axial=true;
rslt_show_z_smooth=false;
rslt_show_z_individual=true;
rslt_show_f_axial=true;
rslt_show_f_smooth=false;
rslt_show_f_individual=true;
rslt_show_smooth_sigma=0.3; // mm
rslt_scan_below=-10.0;
rslt_scan_above= 10.0;
rslt_scan_step= 5.0;
......@@ -301,9 +307,12 @@ public class FocusingField {
properties.setProperty(prefix+"qb_invert",qb_invert+"");
properties.setProperty(prefix+"z_relative",z_relative+"");
properties.setProperty(prefix+"rslt_show_z_axial",rslt_show_z_axial+"");
properties.setProperty(prefix+"rslt_show_z_smooth",rslt_show_z_smooth+"");
properties.setProperty(prefix+"rslt_show_z_individual",rslt_show_z_individual+"");
properties.setProperty(prefix+"rslt_show_f_axial",rslt_show_f_axial+"");
properties.setProperty(prefix+"rslt_show_f_smooth",rslt_show_f_smooth+"");
properties.setProperty(prefix+"rslt_show_f_individual",rslt_show_f_individual+"");
properties.setProperty(prefix+"rslt_show_smooth_sigma",rslt_show_smooth_sigma+"");
properties.setProperty(prefix+"rslt_scan_below",rslt_scan_below+"");
properties.setProperty(prefix+"rslt_scan_above",rslt_scan_above+"");
properties.setProperty(prefix+"rslt_scan_step",rslt_scan_step+"");
......@@ -393,12 +402,18 @@ public class FocusingField {
z_relative=Boolean.parseBoolean(properties.getProperty(prefix+"z_relative"));
if (properties.getProperty(prefix+"rslt_show_z_axial")!=null)
rslt_show_z_axial=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_show_z_axial"));
if (properties.getProperty(prefix+"rslt_show_z_smooth")!=null)
rslt_show_z_smooth=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_show_z_smooth"));
if (properties.getProperty(prefix+"rslt_show_z_individual")!=null)
rslt_show_z_individual=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_show_z_individual"));
if (properties.getProperty(prefix+"rslt_show_f_axial")!=null)
rslt_show_f_axial=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_show_f_axial"));
if (properties.getProperty(prefix+"rslt_show_f_smooth")!=null)
rslt_show_f_smooth=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_show_f_smooth"));
if (properties.getProperty(prefix+"rslt_show_f_individual")!=null)
rslt_show_f_individual=Boolean.parseBoolean(properties.getProperty(prefix+"rslt_show_f_individual"));
if (properties.getProperty(prefix+"rslt_show_smooth_sigma")!=null)
rslt_show_smooth_sigma=Double.parseDouble(properties.getProperty(prefix+"rslt_show_smooth_sigma"));
if (properties.getProperty(prefix+"rslt_scan_below")!=null)
rslt_scan_below=Double.parseDouble(properties.getProperty(prefix+"rslt_scan_below"));
if (properties.getProperty(prefix+"rslt_scan_above")!=null)
......@@ -512,7 +527,7 @@ public boolean configureDataVector(String title, boolean forcenew, boolean enabl
gd.addCheckbox("Filter non-concave areas from best focus for each sample",filterInputConcave);
gd.addNumericField("Concave filter sigma",filterInputConcaveSigma,3,5,"um");
gd.addCheckbox("Remove small series ",filterInputConcaveRemoveFew);
gd.addNumericField("Minimal number of samples (to remove / apply concave vilter) ",filterInputConcaveMinSeries,3,5,"samples");
gd.addNumericField("Minimal number of samples (to remove / apply concave filter) ",filterInputConcaveMinSeries,3,5,"samples");
gd.addNumericField("Concave filter sigma",filterInputConcaveScale,3,5,"<=1.0");
gd.addCheckbox("Sagittal channels are master channels (false - tangential are masters)",sagittalMaster);
......@@ -807,6 +822,24 @@ private boolean [] filterConcave(
enable_out[thisIndices[i]]=false;
numFiltered++;
}
// See if too few are left - remove them
int numPointsLeft=0;
for (int i=0;i<thisIndices.length;i++) if (enable_out[thisIndices[i]]){
numPointsLeft++;
}
if (numPointsLeft<minSeries){
if (debugLevel>0) System.out.println("filterConcave(): Channel "+chn+" sample "+sample+" has too few points left after filter - "+numPointsLeft+" < "+minSeries);
if (removeInsufficient){
for (int i=0;i<indices[chn][sample].length;i++){
if (enable_out[thisIndices[i]]) {
enable_out[indices[chn][sample][i]]=false;
numFilteredInsufficient++;
}
}
}
}
if (debugLevel>debugThreshold) {
System.out.println("filterConcave(), chn="+chn+", sample="+sample);
......@@ -1768,6 +1801,34 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
}
public void compareDrDerivatives(double [] vector){
double delta=0.00010; // make configurable
if (debugParameter>=0){
String parName="";
if ((debugParameterNames!=null) && (debugParameterNames.length>debugParameter)) parName=debugParameterNames[debugParameter];
System.out.println("Debugging derivatives for parameter #"+debugParameter+" ("+parName+")");
//debugParameterNames
double [] vector_dp=vector.clone();
vector_dp[debugParameter]+=delta;
double [] fx_dp=createFXandJacobian(vector_dp,false);
double [] fx= createFXandJacobian(vector,true);
for (int i=0;i<fx.length;i++){
if ((debugPoint>=0) && (debugPoint!=i)) continue; // debug only single point
int nMeasPoints=dataVector.length;
String pointName="";
if (i<nMeasPoints){
pointName="chn"+dataVector[i].channel+":"+dataVector[i].sampleIndex+"__"+dataVector[i].timestamp;
// } else {
// int overData=i-nMeasPoints;
// if ((corrNames!=null) && (overData< corrNames.length)){
// pointName="correction_parameter-"+corrNames[overData];
// } else {
// pointName="unknown-point_+"+overData;
// }
}
System.out.println(i+": "+pointName+" fx= "+fx[i]+" delta_fx= "+((fx_dp[i]-fx[i])/delta)+" df/dp= "+jacobian[debugParameter][i]);
}
}
/*
boolean [] centerSelect=fieldFitting.getCenterSelect();
if (!centerSelect[0] || !centerSelect[1]){
System.out.println("compareDrDerivatives(): Both px0 and px1 parameters should be enabled, aborting");
......@@ -1785,6 +1846,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
System.out.println(" df/dx= "+jacobian[0][i]+" df/dy= "+jacobian[1][i]);
}
*/
}
......@@ -1821,7 +1883,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
this.lMAArrays=calculateJacobianArrays(this.currentfX);
this.currentRMS= calcErrorDiffY(this.currentfX,false);
this.currentRMSPure=calcErrorDiffY(this.currentfX, true);
msg=": initial RMS="+IJ.d2s(this.currentRMS,8)+" (pure RMS"+IJ.d2s(this.currentRMSPure,8)+")"+
msg=": initial RMS="+IJ.d2s(this.currentRMS,8)+" (pure RMS="+IJ.d2s(this.currentRMSPure,8)+")"+
". Calculating next Jacobian. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length;
if (debugLevel>1) System.out.println(msg);
if (this.updateStatus) IJ.showStatus(msg);
......@@ -2339,29 +2401,42 @@ public void listCombinedResults(){
// public double fwhm_to_mtf50=500.0; // put actual number
double [] center_z=fieldFitting.getZCenters();
GenericDialog gd = new GenericDialog("Setup results table");
double best_qb_axial= fieldFitting.getBestQualB(
k_red,
k_blue,
false);
double best_qb_corr= fieldFitting.getBestQualB(
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]
};
double [] best_qb_axial= fieldFitting.getBestQualB(
k_red,
k_blue,
false);
double [] best_qb_corr= fieldFitting.getBestQualB(
k_red,
k_blue,
true);
gd.addMessage("Best center focus for Red "+ IJ.d2s(center_z[0],3)+" um");
gd.addMessage("Best center focus for Green "+ IJ.d2s(center_z[1],3)+" um");
gd.addMessage("Best center focus for Blue "+ IJ.d2s(center_z[2],3)+" um");
gd.addMessage("Best composite distance for FWHM^4, axial model "+ IJ.d2s(best_qb_axial,3)+" um");
gd.addMessage("Best composite distance for FWHM^4, individual "+ IJ.d2s(best_qb_corr,3)+" um");
GenericDialog gd = new GenericDialog("Setup results table FWHM="+IJ.d2s(best_qb_corr[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/best_qb_corr[1],2)+" lp/mm");
gd.addMessage("Best center focus for Red "+ IJ.d2s(center_z[0],3)+" um"+
", FWHM="+IJ.d2s(centerFWHM[0],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/centerFWHM[0],2)+" lp/mm");
gd.addMessage("Best center focus for Green "+ IJ.d2s(center_z[1],3)+" um"+
", FWHM="+IJ.d2s(centerFWHM[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/centerFWHM[1],2)+" lp/mm");
gd.addMessage("Best center focus for Blue "+ IJ.d2s(center_z[2],3)+" um"+
", FWHM="+IJ.d2s(centerFWHM[2],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/centerFWHM[2],2)+" lp/mm");
gd.addMessage("Best composite distance for FWHM^4, axial model "+ IJ.d2s(best_qb_axial[0],3)+" um"+
", FWHM="+IJ.d2s(best_qb_axial[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/best_qb_axial[1],2)+" lp/mm");
gd.addMessage("Best composite distance for FWHM^4, individual "+ IJ.d2s(best_qb_corr[0],3)+" um"+
", FWHM="+IJ.d2s(best_qb_corr[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/best_qb_corr[1],2)+" lp/mm");
for (int i=0;i<rslt_show_chn.length;i++){
gd.addCheckbox("Show results for "+fieldFitting.getDescription(i), this.rslt_show_chn[i]);
gd.addCheckbox("Show results for "+fieldFitting.getDescription(i), this.rslt_show_chn[i]);
}
gd.addCheckbox("Show best focus distance (axial model)", this.rslt_show_z_axial);
gd.addCheckbox("Show ring-averaged focus distance", this.rslt_show_z_smooth);
gd.addCheckbox("Show best focus distance (per-sample adjusted)", this.rslt_show_z_individual);
gd.addCheckbox("Show constant-z sections (axial model)", this.rslt_show_f_axial);
gd.addCheckbox("Show ring-averaged per-sample adjusted section data", this.rslt_show_f_smooth);
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("Show focal distance relative to center green (false - motor absolute)", this.z_relative);
gd.addCheckbox("Show focal distance relative to center green (false - best_qb_corr[1])", this.z_relative);
gd.addMessage("Multiple section setup:");
gd.addNumericField("Scan from (relative to green center)", this.rslt_scan_below, 3,7,"um");
......@@ -2373,12 +2448,16 @@ public void listCombinedResults(){
}
for (int i=0;i<rslt_show_chn.length;i++){
this.rslt_show_chn[i]=gd.getNextBoolean();
this.rslt_show_chn[i]=gd.getNextBoolean();
}
this.rslt_show_z_axial= gd.getNextBoolean();
this.rslt_show_z_smooth= gd.getNextBoolean();
this.rslt_show_z_individual= gd.getNextBoolean();
this.rslt_show_f_axial= gd.getNextBoolean();
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.z_relative= gd.getNextBoolean();
this.rslt_scan_below= gd.getNextNumber();
......@@ -2388,32 +2467,89 @@ public void listCombinedResults(){
listCombinedResults(
"Field curvature measuremnts results", //String title,
null, //String path,
z_relative?center_z[1]:0.0,
z_relative?best_qb_corr[0]:center_z[1],
rslt_show_chn, //boolean [] show_chn,
rslt_show_z_axial, //boolean show_z_axial,
rslt_show_z_smooth, // boolean rslt_show_z_smooth;
rslt_show_z_individual, //boolean show_z_individual,
rslt_show_f_axial, //boolean show_f_axial,
rslt_show_f_smooth, //boolean rslt_show_f_smooth;
rslt_show_f_individual, //boolean show_f_individual,
rslt_show_smooth_sigma, // double rslt_show_smooth_sigma;
center_z[1]+rslt_scan_below, // double scan_below,
center_z[1]+rslt_scan_above, //double scan_above,
rslt_scan_step, //double scan_step,
rslt_mtf50_mode); //boolean freq_mode)
}
public double [][] filterListSamples(
double sigma,
double [] radiuses, // numsaples+1 long!
double [] saggital, // numsamples!
double []tangential,
double [] saggitalWeights, // numsamples long
double [] tangentialWeights){// numsamples long
double [][] data={saggital,tangential};
double [][] weights={saggitalWeights,tangentialWeights};
int len=saggital.length+1;
double [][] result = new double[2][len];
double kexp=-0.5/(sigma*sigma);
for (int dir=0;dir<2;dir++) {
if (data[dir]!=null) {
result[dir] = new double[len];
for (int i=0;i<len;i++){
double sum_w=0.0;
double sum_v=0.0;
for (int otherDir=0;otherDir<2;otherDir++) {
if (data[otherDir]!=null)
for (int j=1;j<len;j++){
double r= (otherDir==dir)?(radiuses[i]-radiuses[j]):(radiuses[i]+radiuses[j]);
double w=Math.exp(kexp*r*r);
if (weights[otherDir]!=null){
w*=weights[otherDir][j-1];
}
if (!Double.isNaN(data[otherDir][j-1])) {
sum_v+=data[otherDir][j-1]*w;
sum_w+=w;
}
}
}
result[dir][i]=(sum_w>0.0)?(sum_v/sum_w):0.0;
}
} else {
result[dir]=null;
}
}
return result;
}
public void listCombinedResults(
String title,
String path,
double z0, // subtract from z
boolean [] show_chn,
boolean show_z_axial,
boolean show_z_smooth,
boolean show_z_individual,
boolean show_f_axial,
boolean show_f_smooth,
boolean show_f_individual,
double smooth_sigma,
double scan_below,
double scan_above,
double scan_step,
boolean freq_mode){
String [] chnNames={"RS","RT","GS","GT","BS","BT"};
// Calculate weights of each channel/sample
double [][] sampleWeights=new double[getNumChannels()][getNumSamples()];
for (int chn=0;chn<sampleWeights.length;chn++) for (int sample=0;sample<sampleWeights[chn].length;sample++) {
sampleWeights[chn][sample]=0.0;
}
for (int index=0;index<dataVector.length;index++) {
sampleWeights[dataVector[index].channel][dataVector[index].sampleIndex] += dataWeights[index];
}
double k=this.fwhm_to_mtf50; //TODO: correct psf fwhm to mtf50 conversion
// double k=2*Math.log(2.0)/Math.PI*1000;
......@@ -2424,6 +2560,12 @@ public void listCombinedResults(
if (show_chn[i])header+="\tZ"+chnNames[i];
}
}
if (show_z_smooth){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\tZ"+chnNames[i]+"~";
}
}
if (show_z_individual){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\tZ"+chnNames[i]+"*";
......@@ -2436,6 +2578,11 @@ public void listCombinedResults(
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z-z0,1);
}
}
if (show_f_smooth) {
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z-z0,1)+"~";
}
}
if (show_f_individual) {
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z-z0,1)+"*";
......@@ -2448,7 +2595,7 @@ public void listCombinedResults(
double [] radiuses=new double [numSamples+1];
radiuses[0]=0.0;
for (int i=0;i<numSamples;i++) radiuses[i+1]=radiuses0[i];
double [][][][] f_values=new double [numSect][2][][];
double [][][][] f_values=new double [numSect][3][][];
int sect=0;
for (double z=scan_below;z<=scan_above;z+=scan_step){
if (show_f_axial){
......@@ -2482,9 +2629,26 @@ public void listCombinedResults(
} else {
f_values[sect][1]=null;
}
if (show_f_smooth){
double [][] f=fieldFitting.getCalcValuesForZ(z, true,true); // corrected (individual),
f_values[sect][2]=new double [f.length][];
for (int chn=0;chn<f.length;chn+=2){
double [][] smooth=filterListSamples(
smooth_sigma,
radiuses, // all 3 arrays should be numsaples+1 long
f[chn] , //double [] saggital, // not ordered, but [0]==0.0
f[chn+1] , //double []tangential,
sampleWeights[chn], //double [] saggitalWeights, // numsamples long
sampleWeights[chn+1]); //double [] tangentialWeights){// numsamples long
f_values[sect][2][chn]=smooth[0];
f_values[sect][2][chn+1]=smooth[1];
}
} else {
f_values[sect][2]=null;
}
sect++;
}
double [][][] z_values=new double [2][][];
double [][][] z_values=new double [3][][];
if (show_z_axial){
double [][] zai=fieldFitting.getCalcZ(false,true);
double [] zai0=fieldFitting.getCalcZ(0.0);
......@@ -2514,6 +2678,28 @@ public void listCombinedResults(
} else z_values[1][chn]=null;
}
} else z_values[1] = null;
if (show_f_smooth){
double [][] zai=fieldFitting.getCalcZ(true,true);
z_values[2]=new double [zai.length][];
for (int chn=0;chn<zai.length;chn+=2){
double [][] smooth=filterListSamples(
smooth_sigma,
radiuses, // all 3 arrays should be numsaples+1 long
zai[chn] , //double [] saggital, // not ordered, but [0]==0.0
zai[chn+1] , //double []tangential,
sampleWeights[chn], //double [] saggitalWeights, // numsamples long
sampleWeights[chn+1]); //double [] tangentialWeights){// numsamples long
z_values[2][chn]=smooth[0];
z_values[2][chn+1]=smooth[1];
}
} else {
z_values[2]=null;
}
StringBuffer sb = new StringBuffer();
for (int n=0;n<radiuses.length;n++){
sb.append(IJ.d2s(radiuses[n],3));
......@@ -2522,6 +2708,11 @@ public void listCombinedResults(
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[0][i][n]-z0,3));
}
}
if (show_z_smooth){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[2][i][n]-z0,3));
}
}
if (show_z_individual){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[1][i][n]-z0,3));
......@@ -2535,6 +2726,13 @@ public void listCombinedResults(
sb.append("\t"+IJ.d2s(f_values[s][0][i][n],3));
}
}
if (show_f_smooth) for (int i=0;i<show_chn.length;i++) if (show_chn[i]) {
if (freq_mode){
sb.append("\t"+IJ.d2s(k/f_values[s][2][i][n],3));
} else {
sb.append("\t"+IJ.d2s(f_values[s][2][i][n],3));
}
}
if (show_f_individual) for (int i=0;i<show_chn.length;i++) if (show_chn[i]) {
if (freq_mode){
sb.append("\t"+IJ.d2s(k/f_values[s][1][i][n],3));
......@@ -2558,20 +2756,30 @@ public void listCombinedResults(
public void listScanQB(){
double [] center_z=fieldFitting.getZCenters();
double best_qb_axial= fieldFitting.getBestQualB(
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]
};
double [] best_qb_axial= fieldFitting.getBestQualB(
k_red,
k_blue,
false);
double best_qb_corr= fieldFitting.getBestQualB(
double [] best_qb_corr= fieldFitting.getBestQualB(
k_red,
k_blue,
true);
GenericDialog gd = new GenericDialog("Setup quality-B table");
gd.addMessage("Best center focus for Red "+ IJ.d2s(center_z[0],3)+" um");
gd.addMessage("Best center focus for Green "+ IJ.d2s(center_z[1],3)+" um");
gd.addMessage("Best center focus for Blue "+ IJ.d2s(center_z[2],3)+" um");
gd.addMessage("Best composite distance for FWHM^4, axial model "+ IJ.d2s(best_qb_axial,3)+" um");
gd.addMessage("Best composite distance for FWHM^4, individual "+ IJ.d2s(best_qb_corr,3)+" um");
GenericDialog gd = new GenericDialog("Setup quality-B table FWHM="+IJ.d2s(best_qb_corr[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/best_qb_corr[1],2)+" lp/mm");
gd.addMessage("Best center focus for Red "+ IJ.d2s(center_z[0],3)+" um"+
", FWHM="+IJ.d2s(centerFWHM[0],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/centerFWHM[0],2)+" lp/mm");
gd.addMessage("Best center focus for Green "+ IJ.d2s(center_z[1],3)+" um"+
", FWHM="+IJ.d2s(centerFWHM[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/centerFWHM[1],2)+" lp/mm");
gd.addMessage("Best center focus for Blue "+ IJ.d2s(center_z[2],3)+" um"+
", FWHM="+IJ.d2s(centerFWHM[2],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/centerFWHM[2],2)+" lp/mm");
gd.addMessage("Best composite distance for FWHM^4, axial model "+ IJ.d2s(best_qb_axial[0],3)+" um"+
", FWHM="+IJ.d2s(best_qb_axial[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/best_qb_axial[1],2)+" lp/mm");
gd.addMessage("Best composite distance for FWHM^4, individual "+ IJ.d2s(best_qb_corr[0],3)+" um"+
", FWHM="+IJ.d2s(best_qb_corr[1],3)+"um, MTF50="+IJ.d2s(fwhm_to_mtf50/best_qb_corr[1],2)+" lp/mm");
gd.addNumericField("Scan from (relative to green center)", this.qb_scan_below, 3,7,"um");
gd.addNumericField("Scan to (relative to green center)", this.qb_scan_above, 3,7,"um");
gd.addNumericField("Scan step", this.qb_scan_step, 3,7,"um");
......@@ -2579,7 +2787,7 @@ public void listScanQB(){
gd.addNumericField("Relative (to green) weight of blue channel",100* this.k_blue, 3,7,"%");
gd.addCheckbox("Use per-sample location corrected data", this.qb_use_corrected);
gd.addCheckbox("Show mtf50 (false - PSF FWHM)", this.qb_invert);
gd.addCheckbox("Show focal distance relative to center green (false - motor absolute)", this.z_relative);
gd.addCheckbox("Show focal distance relative to best composite focus (false - to center green )", this.z_relative);
gd.showDialog();
if (gd.wasCanceled()) {
......@@ -2598,7 +2806,7 @@ public void listScanQB(){
listScanQB(
"Focus quality vs. distance", // String title,
null, //String path,
z_relative?center_z[1]:0.0,
z_relative?best_qb_corr[0]:center_z[1],
center_z[1]+this.qb_scan_below, //double min_z, // absolute
center_z[1]+this.qb_scan_above, //double max_z,
this.qb_scan_step , //double step_z,
......@@ -2641,6 +2849,31 @@ public void listScanQB(
// for (String s:this.fieldFitting.getParameterValueStrings(true,true)){ //this.showDisabledParams)){ //
// sb.append(s+"\n");
// }
// Add result to the bottom of the file
double [] center_z=fieldFitting.getZCenters();
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]
};
// double [] best_qb_axial= fieldFitting.getBestQualB(
// k_red,
// k_blue,
// false);
double [] best_qb_corr= fieldFitting.getBestQualB(
k_red,
k_blue,
true);
sb.append("Results:\t---\t---\t---\t---\n");
sb.append("Red center"+"\t"+ IJ.d2s(center_z[0],3)+"\t"+IJ.d2s(centerFWHM[0],3)+"\t"+IJ.d2s(fwhm_to_mtf50/centerFWHM[0],2)+"\t"+"lp/mm" +"\n");
sb.append("Green center"+"\t"+IJ.d2s(center_z[1],3)+"\t"+IJ.d2s(centerFWHM[1],3)+"\t"+IJ.d2s(fwhm_to_mtf50/centerFWHM[1],2)+"\t"+"lp/mm" +"\n");
sb.append("Blue center"+"\t"+ IJ.d2s(center_z[2],3)+"\t"+IJ.d2s(centerFWHM[2],3)+"\t"+IJ.d2s(fwhm_to_mtf50/centerFWHM[2],2)+"\t"+"lp/mm" +"\n");
sb.append("Composite ^4"+"\t"+ IJ.d2s(best_qb_corr[0],3)+"\t"+IJ.d2s(best_qb_corr[1],3)+"\t"+IJ.d2s(fwhm_to_mtf50/best_qb_corr[1],2)+"\t"+"lp/mm" +"\n");
sb.append("Lens center "+"\t"+ "used" + "\t"+IJ.d2s(currentPX0,1)+"\t"+ IJ.d2s(currentPY0,1)+"\t"+"pix" +"\n");
sb.append("Lens center "+"\t"+ "distortions" + "\t"+IJ.d2s(pX0_distortions,1)+"\t"+IJ.d2s(pY0_distortions,1)+"\t"+"pix" +"\n");
if (path!=null) {
CalibrationFileManagement.saveStringToFile (
path,
......@@ -3106,7 +3339,11 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
private int [][] sampleCorrChnParIndex=null;
private boolean [] dflt_sampleCorrSelect= {false,false,false,false};
// private double [] dflt_sampleCorrCost= {1.0,50.0,1.0,1.0};
private double [] dflt_sampleCorrCost= {0.3,20.0,0.3,1.0};
// private double [] dflt_sampleCorrCost= {0.3,20.0,0.3,1.0};
// private double [] dflt_sampleCorrCost= {0.05,10.0,2.0,1.0};
// private double [] dflt_sampleCorrCost= {0.05,1.0,1.0,1.0};
// private double [] dflt_sampleCorrCost= {0.5,0.5,2.0,1.0};
private double [] dflt_sampleCorrCost= {0.1,0.5,2.0,1.0};
private double dflt_sampleCorrSigma= 2.0; // mm
private double dflt_sampleCorrPullZero= 0.75; // fraction
public final String [] channelDescriptions={
......@@ -3302,8 +3539,12 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
return sampleCorrRadius;
}
public double getSampleRadius(int sample){
double dx=sampleCoordinates[sample][0]-pXY[0];
double dy=sampleCoordinates[sample][1]-pXY[1];
return getPixelMM()*Math.sqrt(dx*dx+dy*dy);
}
public void showCurvCorr(String title){
int width=getSampleWidth();
......@@ -3378,9 +3619,9 @@ public boolean LevenbergMarquardt(boolean openDialog, int debugLevel){
if ((curvatureModel[chn]!=null) && (allChannels || channelSelect[chn])){
result[chn]=new double [numSamples];
for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) {
if ((chn==3) && (sampleIndex==23)){
System.out.println("getCalcValuesForZ(), chn="+chn+", sampleIndex="+sampleIndex);
}
//if ((chn==3) && (sampleIndex==23)){
// System.out.println("getCalcValuesForZ(), chn="+chn+", sampleIndex="+sampleIndex);
//}
result[chn][sampleIndex]=curvatureModel[chn].getFdF(
corrected?getCorrPar(chn,sampleIndex):null,
......@@ -3400,13 +3641,81 @@ if ((chn==3) && (sampleIndex==23)){
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]=curvatureModel[chn].getAr(r, null)[0];
result[chn]=findBestZ(chn, -1, false);
} else {
result[chn]=Double.NaN;
}
}
return result;
}
public double findBestZ(
int channel,
int sampleIndex, // -1 for center
boolean corrected){
return findBestZ(
channel,
sampleIndex, // -1 for center
corrected, //
1.0, // double iniStep,
0.0001); //double precision)
}
public double findBestZ(
int channel,
int sampleIndex, // -1 for center
boolean corrected, //
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 (Double.isNaN(z0)) return z0;
double f0=getCalcValuesForZ(z0, r)[channel];
double z1=z0+iniStep;
double f1=getCalcValuesForZ(z1,r)[channel];
double dir = (f1<f0)?1.0:-1.0;
double z_prev,f_prev;
if (dir>0) {
z_prev=z0;
f_prev=f0;
z0=z1;
f0=f1;
} else {
z_prev=z1;
f_prev=f1;
}
int step;
for (step=0;step<maxSteps;step++) {
z1=z0+dir*iniStep;
f1=getCalcValuesForZ(z1,r)[channel];
if (f1>f0) break;
z_prev=z0;
f_prev=f0;
z0=z1;
f0=f1;
}
if (step>=maxSteps){
System.out.println("Failed to find minimum in "+maxSteps+" steps");
return Double.NaN;
}
// now dividing z_prev - z0 - z1 range
for (step=0;step<maxSteps;step++) {
if (f_prev>f1){
z_prev=z0;
f_prev=f0;
} else {
z1=z0;
f1=f0;
}
z0=(z_prev+z1)/2;
// f0=getCalcValuesForZ(z1,r)[channel]; // ????
f0=getCalcValuesForZ(z0,r)[channel];
if (Math.abs(z0-z_prev)<precision) break;
}
return z0;
}
/**
* calculate distance to "best focus" for each channel (color and S/T) for each sample
......@@ -3428,10 +3737,18 @@ if ((chn==3) && (sampleIndex==23)){
result[chn]=new double [numSamples];
for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) {
if (goodSamples[chn][sampleIndex]) {
/*
result[chn][sampleIndex]=curvatureModel[chn].getAr(
sampleCorrRadius[sampleIndex],
corrected?getCorrPar(chn,sampleIndex):null
)[0];
//That was just the initial estimation, true only if z^1... are all 0
*/
result[chn][sampleIndex]=findBestZ(
chn, // int channel,
sampleIndex, // int sampleIndex,
corrected); //boolean corrected,
} else {
result[chn][sampleIndex]=Double.NaN;
}
......@@ -3449,10 +3766,17 @@ if ((chn==3) && (sampleIndex==23)){
}
public double [] getZCenters(){
// int chn=3; // Green, Tangential
double [] result = {
/* double [] result = {
curvatureModel[1].getCenterVector()[0], // Red, Tangential
curvatureModel[3].getCenterVector()[0], // Green, Tangential
curvatureModel[5].getCenterVector()[0]}; // Blue, Tangential
*/
double [] result = {
findBestZ(1, -1, false),
findBestZ(3, -1, false),
findBestZ(5, -1, false),
};
return result;
}
public double [] getQualB(double z, boolean corrected){
......@@ -3518,7 +3842,7 @@ if ((chn==3) && (sampleIndex==23)){
(k[0]+k[1]+k[2])));
}
public double getBestQualB(
public double [] getBestQualB(
double kr,
double kb,
boolean corrected){
......@@ -3526,7 +3850,7 @@ if ((chn==3) && (sampleIndex==23)){
}
public double getBestQualB( // find minimum
public double [] getBestQualB( // find minimum
double kr,
double kb,
boolean corrected,
......@@ -3539,43 +3863,47 @@ if ((chn==3) && (sampleIndex==23)){
double qb1=getQualB(z1,kr,kb,corrected);
double dir = (qb1<qb0)?1.0:-1.0;
double z_prev,qb_prev;
double [] result={Double.NaN,Double.NaN};
if (dir>0) {
z_prev=z0;
qb_prev=qb0;
z0=z1;
qb0=qb1;
z_prev=z0;
qb_prev=qb0;
z0=z1;
qb0=qb1;
} else {
z_prev=z1;
qb_prev=qb1;
z_prev=z1;
qb_prev=qb1;
}
int step;
for (step=0;step<maxSteps;step++) {
z1=z0+dir*iniStep;
qb1=getQualB(z1,kr,kb,corrected);
if (qb1>qb0) break;
z_prev=z0;
qb_prev=qb0;
z0=z1;
qb0=qb1;
z1=z0+dir*iniStep;
qb1=getQualB(z1,kr,kb,corrected);
if (qb1>qb0) break;
z_prev=z0;
qb_prev=qb0;
z0=z1;
qb0=qb1;
}
if (step>=maxSteps){
System.out.println("Failed to find minimum in "+maxSteps+" steps");
return Double.NaN;
System.out.println("Failed to find minimum in "+maxSteps+" steps");
return result;
}
// now dividing z_prev - z0 - z1 range
for (step=0;step<maxSteps;step++) {
if (qb_prev>qb1){
z_prev=z0;
qb_prev=qb0;
} else {
z1=z0;
qb1=qb0;
}
z0=(z_prev+z1)/2;
qb0=getQualB(z1,kr,kb,corrected);
if (Math.abs(z0-z_prev)<precision) break;
if (qb_prev>qb1){
z_prev=z0;
qb_prev=qb0;
} else {
z1=z0;
qb1=qb0;
}
z0=(z_prev+z1)/2;
// qb0=getQualB(z1,kr,kb,corrected); // ???????????????????
qb0=getQualB(z0,kr,kb,corrected);
if (Math.abs(z0-z_prev)<precision) break;
}
return z0;
result[0]=z0;
result[1]=qb0;
return result; // z0;
}
......@@ -3838,12 +4166,13 @@ if ((chn==3) && (sampleIndex==23)){
double dx=sampleCoordinates[i][0]-sampleCoordinates[i][0];
double dy=sampleCoordinates[i][1]-sampleCoordinates[i][1];
double a= Math.exp(k*(dx*dx+dy*dy));
if (a<0.01) a=0.0; // reduce numbner of non-zero matrix elements
sampleCorrCrossWeights[nChn][nPar][i][j]=a;
sw+=a;
}
}
double normalizedCost=sampleCorrCost[nChn][nPar];
if (sampleSeriesWeights!=null) normalizedCost*=sampleSeriesWeights[nChn][i];
if ((sampleSeriesWeights!=null) && ((sampleSeriesWeights[nChn][i]!=0.0))) normalizedCost*=sampleSeriesWeights[nChn][i];
if ((sampleCorrPullZero[nChn][nPar]==0) ||(sampleCorrCost[nChn][nPar]==0)) sw=0.0;
else if (sw!=0.0) sw=-normalizedCost*sampleCorrPullZero[nChn][nPar]/sw;
for (int j=0;j<numberOfLocations;j++) {
......@@ -4405,7 +4734,7 @@ if ((chn==3) && (sampleIndex==23)){
for (int i=0;i<2;i++){
dr_dxy[i]*=getPixelMM(); // radius in mm, dx, dy - in pixels
}
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){ // c -full, nChn - disabled skipped - dependent COMPONET
boolean isMasterDir=(c%2) == (sagittalMaster?0:1);
int otherChannel= c ^ 1;
// deriv[nChn]=new double [getNumberOfRegularParameters(sagittalMaster)]; //???????????
......@@ -4427,13 +4756,14 @@ if ((chn==3) && (sampleIndex==23)){
}
}
// other parameters - for dependent - skip center (j==0), for master add dependent
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){ // n - group of channel parameters
int [] ncp=curvatureModel[n].getNumPars(); // {(z),(r)}
boolean isDependMasterDir=(n%2) == (sagittalMaster?0:1);
for (int i=0;i<curvatureSelect[n].length; i++) if (curvatureSelect[n][i] ){
if (((i%ncp[1])!=0) || isDependMasterDir) {
boolean isDependMasterDir=(n%2) == (sagittalMaster?0:1); // n is master
for (int i=0;i<curvatureSelect[n].length; i++) if (curvatureSelect[n][i] ){ // i - parameter number
if (((i%ncp[1])!=0) || isDependMasterDir) { // non center or master
int dependOnChannel=(((i%ncp[1])==0) && !isMasterDir)?otherChannel:c;
deriv[nChn][np++]=(n==dependOnChannel)?(deriv_curv[n][i]):0.0;
deriv[nChn][np++]=(n==dependOnChannel)?(deriv_curv[c][i]):0.0; // deriv[nChn][np++]=(n==dependOnChannel)?(deriv_curv[n][i]):0.0;
}
}
}
......@@ -5140,7 +5470,7 @@ ar1 - ar[4]
return f; // function value
}
public String getRadialName(int i){
return "ar_"+(i+1);
return "ar_"+(i+1); //TODO: chnage ar_1-> ar_0 (or ar_c),but that will break configuration files
}
public String getRadialDecription(int i){
if (i==0) return "Radial constant coefficient";
......
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