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imagej-elphel
Commit fd3a84bd authored by Andrey Filippov's avatar Andrey Filippov
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minor bug fixes

parent 7861f591
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Showing with 66 additions and 38 deletions
src/main/java/FocusingField.java
View file @ fd3a84bd
......@@ -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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