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Commit 57f9aca9 authored by Andrey Filippov's avatar Andrey Filippov
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parent 47ffc516
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Showing with 599 additions and 138 deletions
src/main/java/Aberration_Calibration.java
View file @ 57f9aca9
......@@ -10147,6 +10147,9 @@ if (MORE_BUTTONS) {
}
}
boolean showPSF=debugLevel>1;
if (metrics==null) return null;
if (showPSF || (focusMeasurementParameters.saveResults)){
double [][][][] psfRGB=new double [psf_kernels.length][psf_kernels[0].length][][];
// reorder and assign names to kernel color channels
......@@ -10189,8 +10192,11 @@ if (MORE_BUTTONS) {
imp_psf.setProperty("pY_"+index, ""+sampleCoord[ii][jj][1]);
if (fullResults[ii][jj]!=null){
for (int cc=0;cc<fullResults[ii][jj].length;cc++) if (fullResults[ii][jj][cc]!=null){
imp_psf.setProperty("R50_"+cc+"_"+index, ""+fullResults[ii][jj][cc][0]);
imp_psf.setProperty("RTratio_"+cc+"_"+index, ""+fullResults[ii][jj][cc][1]);
// imp_psf.setProperty("R50_"+cc+"_"+index, ""+fullResults[ii][jj][cc][0]);
// imp_psf.setProperty("RTratio_"+cc+"_"+index, ""+fullResults[ii][jj][cc][1]);
imp_psf.setProperty("R50_x2_"+cc+"_"+index, ""+fullResults[ii][jj][cc][0]);
imp_psf.setProperty("R50_y2_"+cc+"_"+index, ""+fullResults[ii][jj][cc][1]);
imp_psf.setProperty("R50_xy_"+cc+"_"+index, ""+fullResults[ii][jj][cc][2]);
}
}
}
......@@ -10276,7 +10282,7 @@ if (MORE_BUTTONS) {
fullResults[i][j]=new double [numColors][];
for (int cc=0;cc<numColors;cc++) fullResults[i][j][cc]=null;
}
if (fullResults!=null) fullResults[i][j][color]=new double[2];
// if (fullResults!=null) fullResults[i][j][color]=new double[2];
double x=(sampleCoord[i][j][0]-x0);
double y=(sampleCoord[i][j][1]-y0);
double r=Math.sqrt(x*x+y*y);
......@@ -10287,6 +10293,7 @@ if (MORE_BUTTONS) {
// " psf_cutoffLevel="+focusMeasurementParameters.psf_cutoffLevel+
// " psf_minArea="+focusMeasurementParameters.psf_minArea+
// " psf_blurSigma="+focusMeasurementParameters.psf_blurSigma);
/*
double [] tanRad= matchSimulatedPattern.tangetRadialSizes(
ca, // cosine of the center to sample vector
sa, // sine of the center to sample vector
......@@ -10302,9 +10309,50 @@ if (MORE_BUTTONS) {
tanRad=new double[2];
tanRad[0]=Double.NaN;
tanRad[1]=Double.NaN;
} else {
// debug calculations
double [] x2y2xy= matchSimulatedPattern.x2y2xySizes(
psf[i][j][color], // PSF function, square array, nominally positive
focusMeasurementParameters.psf_cutoffEnergy, // fraction of energy in the pixels to be used
focusMeasurementParameters.psf_cutoffLevel, // minimal level as a fraction of maximal
focusMeasurementParameters.psf_minArea, // minimal selected area in pixels
focusMeasurementParameters.psf_blurSigma, // optionally blur the selection
0.1, //maskCutOff,
debugLevel-2, // debug level
i+":"+j+"["+color+"]"); // String title) { // prefix used for debug images
double [] tanRad1={
Math.sqrt(sa*sa*x2y2xy[0]+ca*ca*x2y2xy[1]-2*ca*sa*x2y2xy[2]),
Math.sqrt(ca*ca*x2y2xy[0]+sa*sa*x2y2xy[1]+2*ca*sa*x2y2xy[2])};
System.out.println("i="+i+" j="+j+" tanRad[0]="+tanRad[0]+ "("+tanRad1[0]+")"+
" tanRad[1]="+tanRad[1]+ "("+tanRad1[1]+") ### "+x2y2xy[0]+", "+x2y2xy[1]+", "+x2y2xy[2]);
}
tanRad[0]/=(focusMeasurementParameters.subdiv/2); // to sesnor pixels
tanRad[1]/=(focusMeasurementParameters.subdiv/2);
*/
double [] x2y2xy= matchSimulatedPattern.x2y2xySizes(
psf[i][j][color], // PSF function, square array, nominally positive
focusMeasurementParameters.psf_cutoffEnergy, // fraction of energy in the pixels to be used
focusMeasurementParameters.psf_cutoffLevel, // minimal level as a fraction of maximal
focusMeasurementParameters.psf_minArea, // minimal selected area in pixels
focusMeasurementParameters.psf_blurSigma, // optionally blur the selection
0.1, //maskCutOff,
debugLevel-2, // debug level
i+":"+j+"["+color+"]"); // String title) { // prefix used for debug images
if (x2y2xy==null){
x2y2xy=new double[3];
for (int ii=0;ii<3;ii++) x2y2xy[ii]=Double.NaN;
} else {
for (int ii=0;ii<x2y2xy.length;ii++) x2y2xy[ii]/=focusMeasurementParameters.subdiv*focusMeasurementParameters.subdiv/4;
}
/*
double [] tanRad={
Math.sqrt(sa*sa*x2y2xy[0]+ca*ca*x2y2xy[1]-2*ca*sa*x2y2xy[2]),
Math.sqrt(ca*ca*x2y2xy[0]+sa*sa*x2y2xy[1]+2*ca*sa*x2y2xy[2])};
*/
// tanRad[0]/=(focusMeasurementParameters.subdiv/2); // to sesnor pixels
// tanRad[1]/=(focusMeasurementParameters.subdiv/2);
double [][]quadCoeff=matchSimulatedPattern.approximatePSFQuadratic(
psf[i][j][color], // PSF function, square array, nominally positive
......@@ -10411,13 +10459,10 @@ Reff=sqrt(1/sqrt(Ar*Br-(Cr/2)^2))
SFcenter+=R50; // only center samples
}
if (fullResults!=null){
// fullResults[i][j][color][0]=R50/(focusMeasurementParameters.subdiv/2); // pixels
// fullResults[i][j][color][1]=BA; // radial-to-tangential ratio - was fullResults[i][j][color][0] ???
fullResults[i][j][color][0]=Math.sqrt((tanRad[0]*tanRad[0]+tanRad[1]*tanRad[1])/2); // sensor pixels
fullResults[i][j][color][1]=tanRad[1]/tanRad[0]; // radial-to-tangential ratio
// fullResults[i][j][color][0]=Math.sqrt((tanRad[0]*tanRad[0]+tanRad[1]*tanRad[1])/2); // sensor pixels
// fullResults[i][j][color][1]=tanRad[1]/tanRad[0]; // radial-to-tangential ratio
fullResults[i][j][color]=x2y2xy.clone();
}
......@@ -10426,7 +10471,8 @@ Reff=sqrt(1/sqrt(Ar*Br-(Cr/2)^2))
for (int k=0;k<quadCoeff[0].length;k++) debugStr+=" "+quadCoeff[0][k];
if (debugLevel>3)System.out.println(debugStr);
System.out.println(i+":"+j+"["+color+"] x="+IJ.d2s(x,1)+" y="+IJ.d2s(y,1)+" xc="+IJ.d2s(xc,2)+" yc="+IJ.d2s(yc,2)+
" tan="+IJ.d2s(tanRad[0],3)+" rad="+IJ.d2s(tanRad[1],3)+
// " tan="+IJ.d2s(tanRad[0],3)+" rad="+IJ.d2s(tanRad[1],3)+
"x2="+IJ.d2s(x2y2xy[0],3)+"y2="+IJ.d2s(x2y2xy[1],3)+"xy="+IJ.d2s(x2y2xy[2],3)+
" Ar="+IJ.d2s(Ar,3)+" Br="+IJ.d2s(Br,3)+" Cr="+IJ.d2s(Cr,3)+ " **** Br/Ar="+IJ.d2s(Br/Ar,3)+" R50="+IJ.d2s(R50,3)+" subpixels" +" A50="+IJ.d2s(Math.sqrt(A50),2)+" subpixels" +" B50=" + IJ.d2s(Math.sqrt(B50),3)+" subpixels");
}
}
......@@ -14959,6 +15005,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
false, // use linear approximation (instead of quadratic)
1.0E-10, // thershold ratio of matrix determinant to norm for linear approximation (det too low - fail)
1.0E-20); // thershold ratio of matrix determinant to norm for quadratic approximation (det too low - fail)
if (distPatPars==null) return null;
int [] iUV={(int) Math.floor(distPatPars[0][2]),(int) Math.floor(distPatPars[1][2])};
boolean negative=((iUV[0]^iUV[1])&1)!=0;
double [] simCorr={
......
src/main/java/CalibrationHardwareInterface.java
View file @ 57f9aca9
......@@ -5525,18 +5525,19 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
if ((samples[ii][jj]!=null) && (samples[ii][jj].length>0)) {
String sdata=ii+sep+jj;
for (int cc=0;cc<samples[ii][jj].length;cc++) {
/*
double rt=samples[ii][jj][cc][0]/Math.sqrt((1+samples[ii][jj][cc][1]*samples[ii][jj][cc][1])/2.0); // tangential;
double rs=rt*samples[ii][jj][cc][1]; // saggital
sdata += sep+rs+ // saggital
sep+rt; // tangential
*/
sdata += sep+samples[ii][jj][cc][0]+ // x2
sep+samples[ii][jj][cc][1]+ // y2
sep+samples[ii][jj][cc][2]; // xy
// double [] samples_st={
// samples[ii][jj][cc][0], // saggital
// samples[ii][jj][cc][0]/samples[ii][jj][cc][1] // tangential (was ratio)
// };
if ((samples[ii][jj]!=null) && (samples[ii][jj][cc]!=null)) {
// hConfig.addProperty(prefix+"y"+ii+".x"+jj+".c"+cc,samples_st); // array of 2
// nodeList.add(sdata);
}
}
nodeList.add(sdata);
}
......@@ -5599,14 +5600,18 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
if (showIndividualSamples){
if (showIndividualComponents) { // additional 3 per-color rows
for (int i=0;i<sampleRows;i++) for (int j=0;j<sampleColumns;j++){
header+="\tY"+i+"X"+j+"_R"+"\tY"+i+"X"+j+"_R/T";
// header+="\tY"+i+"X"+j+"_R"+"\tY"+i+"X"+j+"_R/T";
header+="\tY"+i+"X"+j+"_X2"+"\tY"+i+"X"+j+"_Y2"+"\tY"+i+"X"+j+"_XY";
}
} else {
for (int i=0;i<sampleRows;i++) for (int j=0;j<sampleColumns;j++){ // single row fro all colors
header+="\tY"+i+"X"+j+"_Red_R"+"\tY"+i+"X"+j+"_Red_R/T"+
"\tY"+i+"X"+j+"_Green_R"+"\tY"+i+"X"+j+"_Green_R/T"+
"\tY"+i+"X"+j+"_Blue_R"+"\tY"+i+"X"+j+"_Blue_R/T";
// header+="\tY"+i+"X"+j+"_Red_R"+"\tY"+i+"X"+j+"_Red_R/T"+
// "\tY"+i+"X"+j+"_Green_R"+"\tY"+i+"X"+j+"_Green_R/T"+
// "\tY"+i+"X"+j+"_Blue_R"+"\tY"+i+"X"+j+"_Blue_R/T";
header+="\tY"+i+"X"+j+"_Red_X2"+"\tY"+i+"X"+j+"_Red_Y2"+"\tY"+i+"X"+j+"_Red_XY"+
"\tY"+i+"X"+j+"_Green_X2"+"\tY"+i+"X"+j+"_Green_Y2"+"\tY"+i+"X"+j+"_Green_XY"+
"\tY"+i+"X"+j+"_Blue_X2"+"\tY"+i+"X"+j+"_Blue_Y2"+"\tY"+i+"X"+j+"_Blue_XY";
}
}
}
......@@ -5675,8 +5680,9 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
if ((samples[ii][jj]!=null) && (samples[ii][jj][c]!=null)) {
sb.append( "\t"+IJ.d2s(samples[ii][jj][c][0],3));
sb.append( "\t"+IJ.d2s(samples[ii][jj][c][1],3));
sb.append( "\t"+IJ.d2s(samples[ii][jj][c][2],3));
} else {
sb.append( "\t---\t---");
sb.append( "\t---\t---\t---");
}
}
}
......@@ -5755,8 +5761,9 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
if ((samples[ii][jj]!=null) && (samples[ii][jj][cc]!=null)) {
sb.append( "\t"+IJ.d2s(samples[ii][jj][cc][0],3));
sb.append( "\t"+IJ.d2s(samples[ii][jj][cc][1],3));
sb.append( "\t"+IJ.d2s(samples[ii][jj][cc][2],3));
} else {
sb.append( "\t---\t---");
sb.append( "\t---\t---\t---");
}
}
}
......
src/main/java/FocusingField.java
View file @ 57f9aca9
......@@ -55,8 +55,10 @@ public class FocusingField {
public String serialNumber;
public String lensSerial; // if null - do not add average
public String comment;
public double pX0;
public double pY0;
public double pX0_distortions;
public double pY0_distortions;
public double currentPX0;
public double currentPY0;
public double [][][] sampleCoord;
public ArrayList<FocusingFieldMeasurement> measurements;
boolean sagittalMaster=false; // center data is the same, when true sagittal fitting only may change r=0 coefficients,
......@@ -111,6 +113,7 @@ public class FocusingField {
private boolean showAllSamples = true;
private boolean showIgnoredData= false;
private boolean showRad = true;
private boolean [][][][] sampleMask=null;
public class LMAArrays { // reuse from Distortions?
......@@ -153,6 +156,8 @@ public class FocusingField {
public double py;
public int channel;
public double value;
public double [] dPxyc=new double[2]; // derivative of the value by optical (aberration) center pixel X,Y
// public double weight;
// public MeasuredSample(){}
public MeasuredSample(
......@@ -161,7 +166,9 @@ public class FocusingField {
double px,
double py,
int channel,
double value
double value,
double dPxc,
double dPyc
){
this.motors = motors;
this.timestamp=timestamp;
......@@ -169,6 +176,8 @@ public class FocusingField {
this.py = py;
this.channel = channel;
this.value = value;
this.dPxyc[0]=dPxc;
this.dPxyc[1]=dPyc;
}
}
public boolean configureDataVector(String title, boolean forcenew){
......@@ -200,7 +209,7 @@ public class FocusingField {
gd.addCheckbox("Discard measurements with PSF radius above specified above threshold",useThresholdMax);
if (forcenew) {
gd.addMessage("=== Setting number of parameters for approximation of the PSF dimensions ===");
gd.addNumericField("Number of parameters for pzf(z) approximation (>=3)",numCurvPars[0],0);
gd.addNumericField("Number of parameters for psf(z) approximation (>=3)",numCurvPars[0],0);
gd.addNumericField("Number of parameters for radial dependence of PSF curves (>=1)",numCurvPars[1],0);
}
gd.addMessage("");
......@@ -231,14 +240,17 @@ public class FocusingField {
showDisabled= gd.getNextBoolean();
if (forcenew) {
this.fieldFitting= new FieldFitting(
pX0,
pY0,
currentPX0,
currentPY0,
numCurvPars[0],
numCurvPars[1]);
}
if (setupMasks) this.fieldFitting.maskSetDialog("Setup parameter masks");
if (setupParameters) this.fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled);
this.savedVector=this.fieldFitting.createParameterVector(sagittalMaster);
if (setupMasks) fieldFitting.maskSetDialog("Setup parameter masks");
if (setupParameters) fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled);
double [] centerXY=fieldFitting.getCenterXY();
currentPX0=centerXY[0];
currentPY0=centerXY[1];
this.savedVector=fieldFitting.createParameterVector(sagittalMaster);
// initialVector
return true;
}
......@@ -273,16 +285,34 @@ public class FocusingField {
default: dataWeights[i]=1.0;
}
if (weightRadius>0.0){
double r2=(ms.px-pX0)*(ms.px-pX0)+(ms.py-pY0)*(ms.py-pY0);
double r2=(ms.px-currentPX0)*(ms.px-currentPX0)+(ms.py-currentPY0)*(ms.py-currentPY0);
dataWeights[i]*=Math.exp(kw*r2);
}
// sumWeights+=dataWeights[i];
}
}
// for compatibility with Distortions class
public double [] createFXandJacobian( double [] vector, boolean createJacobian){
// for compatibility with Distortions class\
public void commitParameterVector(double [] vector){
fieldFitting.commitParameterVector(vector,sagittalMaster);
// recalculate measured S,T (depend on center) if center is among fitted parameters
boolean [] centerSelect=fieldFitting.getCenterSelect();
if (centerSelect[0] ||centerSelect[1]){ // do not do that if XC, YC are not modified
// recalculate data vector
double [] pXY=fieldFitting.getCenterXY();
currentPX0=pXY[0];
currentPY0=pXY[1];
setDataVector(createDataVector(
false, // boolean updateSelection,
pXY[0], //double centerPX,
pXY[1])); //double centerPY
}
}
public double [] createFXandJacobian( double [] vector, boolean createJacobian){
commitParameterVector(vector);
return createFXandJacobian(createJacobian);
}
......@@ -322,8 +352,15 @@ public class FocusingField {
for (int i=0;i<numPars;i++){
jacobian[i][n]=derivs[selChanIndices[ms.channel]][i];
}
}
//TODO: correct /dpx, /dpy to compensate for measured S,T calcualtion
boolean [] centerSelect=fieldFitting.getCenterSelect();
if (centerSelect[0] || centerSelect[1]){ // do not do that if both X and Y are disabled
int np=0;
for (int i=0;i<2;i++) if (centerSelect[i]){
jacobian[np++][n]-=ms.dPxyc[i]; // subtract, as effect is opposite to fX
}
}
}
}
return fx;
}
......@@ -341,9 +378,21 @@ public class FocusingField {
}
return Math.sqrt(sum);
}
public MeasuredSample [] createDataVector(){ // use this data
public MeasuredSample [] createDataVector(){
return createDataVector(
true, // boolean updateSelection,
currentPX0, // double centerPX,
currentPY0); //double centerPY
}
public MeasuredSample [] createDataVector(
boolean updateSelection,
double centerPX,
double centerPY
){ // use this data
return createDataVector(
updateSelection,
centerPX,
centerPY,
(this.useMinMeas?this.minMeas:null), // pixels
(this.useMaxMeas?this.maxMeas:null), // pixels
(this.useThresholdMax?this.thresholdMax:null)); // pixels
......@@ -354,18 +403,115 @@ public class FocusingField {
* @param minMeas minimal measurement PSF radius (in pixels) - correction that increases result
* resolution in "sharp" areas (to compensate for measurement error). Individual for each of
* the 6 color/direction components.
* @param updateSelection when true - updates selection of "good" samples, when false - reuses existent one
* @param maxMeas maximal measurement PSF radius (in pixels) - correction that decreases result
* resolution out-of-focus areas to compensate for the limited size of the PSF window.
* Individual for each of the 6 color/direction components.
* @param thresholdMax maximal PSF radius to consider data usable
* @return array of the MeasuredSample instances, including motors, PSF radius, channel and value
*/
/*
Need to find partial derivatives of each of the 3 coefficients: c2, s2 and cs for both px0 and py0
r2 = (x-x0)^2+ (y-y0)^2
c2=(x-x0)^2/r2
s2=(y-y0)^2/r2
cs=(x-x0)*(y-y0)/r2
(p/q)'=(p'*q-q'*p)/q^2
d_r2/d_x0=-2*(x-x0)
d_r2/d_y0=-2*(y-y0)
d_c2/d_x0=(2*(x-x0)*(-1)*r2 - ((d_r2/d_x0)*(x-x0)^2))/r2^2=
(-2*(x-x0)*r2 + (2*(x-x0)*(x-x0)^2))/r2^2=
2*delta_x*(delta_x^2 - r2)/r2^2
d_c2/d_y0= (0-((d_r2/d_y0)*(x-x0)^2))/r2^2=
((2*(y-y0))*(x-x0)^2)/r2^2=
2*delta_y*delta_x^2/r2^2
d_cs/dx0=(-(y-y0)*r2- ((d_r2/d_x0)*(x-x0)*(y-y0)))/r2^2=
(-(y-y0)*r2 + 2*(x-x0)*(x-x0)*(y-y0))/r2^2=
(-delta_y*r2 + 2*delta_x^2*delta_y)/r2^2=
delta_y*(2*delta_x^2-r2)/r2^2
d_c2/d_x0= 2*delta_x*(delta_x^2 - r2)/r2^2
d_c2/d_y0= 2*delta_y*delta_x^2/r2^2
d_s2/d_y0= 2*delta_y*(delta_y^2 - r2)/r2^2
d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
d_cs/dx0= delta_y*(2*delta_x^2-r2)/r2^2
d_cs/dy0= delta_x*(2*delta_y^2-r2)/r2^2
*/
public MeasuredSample [] createDataVector(
boolean updateSelection,
double centerPX,
double centerPY,
double [] minMeas, // pixels
double [] maxMeas, // pixels
double [] thresholdMax){ // pixels
currentPX0=centerPX;
currentPY0=centerPY;
final int numColors=3;
final int numDirs=2;
if (sampleMask== null) updateSelection=true;
if (updateSelection){
sampleMask= new boolean[sampleCoord.length][sampleCoord[0].length][numColors][numDirs];
for (int i=0;i<sampleMask.length;i++)
for (int j=0;j<sampleMask[i].length;j++)
for (int c=0;c<numColors;c++)
for (int d=0;d<numDirs;d++) sampleMask[i][j][c][d]=false;
}
/*
d_c2/d_x0= 2*delta_x*(delta_x^2 - r2)/r2^2
d_c2/d_y0= 2*delta_y*delta_x^2/r2^2
d_s2/d_y0= 2*delta_y*(delta_y^2 - r2)/r2^2
d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
2*d_cs/dx0= 2*delta_y*(2*delta_x^2-r2)/r2^2
2*d_cs/dy0= 2*delta_x*(2*delta_y^2-r2)/r2^2
*/
double [][][] cosSin2Tab=new double[sampleCoord.length][sampleCoord[0].length][3];
double [][][] cosSin2Tab_dx0=new double[sampleCoord.length][sampleCoord[0].length][3];
double [][][] cosSin2Tab_dy0=new double[sampleCoord.length][sampleCoord[0].length][3];
for (int i=0;i<sampleMask.length;i++) for (int j=0;j<sampleMask[i].length;j++){
double delta_x=sampleCoord[i][j][0]-currentPX0;
double delta_y=sampleCoord[i][j][1]-currentPY0;
double r2=delta_x*delta_x+delta_y*delta_y;
double r4=r2*r2;
if (r2>0.0) {
cosSin2Tab[i][j][0]= delta_x*delta_x/r2; // cos^2
cosSin2Tab[i][j][1]= delta_y*delta_y/r2; // sin^2
cosSin2Tab[i][j][2]=2*delta_x*delta_y/r2; // 2*cos*sin
cosSin2Tab_dx0[i][j][0]= 2*delta_x*(delta_x*delta_x - r2)/r4; // d(cos^2)/d(x0)
cosSin2Tab_dx0[i][j][1]= 2*delta_x*delta_y*delta_y/r4; // d(sin^2)/d(x0)
cosSin2Tab_dx0[i][j][2]= 2*delta_y*(2*delta_x*delta_x-r2)/r4; // d(2*cos*sin)/d(x0)
cosSin2Tab_dy0[i][j][0]= 2*delta_y*delta_x*delta_x/r4; // d(cos^2)/d(y0)
cosSin2Tab_dy0[i][j][1]= 2*delta_y*(delta_y*delta_y - r2)/r4; // d(sin^2)/d(y0)
cosSin2Tab_dy0[i][j][2]= 2*delta_x*(2*delta_y*delta_y-r2)/r4; // d(2*cos*sin)/d(y0)
} else {
cosSin2Tab[i][j][0]=1.0;
cosSin2Tab[i][j][1]=0.0;
cosSin2Tab[i][j][2]=0.0;
cosSin2Tab_dx0[i][j][0]=0.0;
cosSin2Tab_dx0[i][j][1]=0.0;
cosSin2Tab_dx0[i][j][2]=0.0;
cosSin2Tab_dy0[i][j][0]=0.0;
cosSin2Tab_dy0[i][j][1]=0.0;
cosSin2Tab_dy0[i][j][2]=0.0;
}
}
ArrayList<MeasuredSample> sampleList=new ArrayList<MeasuredSample>();
if (thresholdMax != null){
weightReference=thresholdMax.clone();
......@@ -392,6 +538,7 @@ public class FocusingField {
}
// convert to microns from pixels
weightReference[c]*=getPixelUM();
System.out.println("==== weightReference["+c+"]="+weightReference[c]);
}
} else {
thresholdMax=null;
......@@ -401,44 +548,103 @@ public class FocusingField {
if (samples!=null) for (int i=0;i<sampleCoord.length;i++){
if ((i<samples.length) && (samples[i]!=null)) for (int j=0;j<sampleCoord[i].length;j++){
if ((j<samples[i].length) && (samples[i][j]!=null)) for (int c=0;c<numColors;c++){
if ((c<samples[i][j].length) && (samples[i][j][c]!=null)) for (int d=0;d<numDirs;d++){
int chn=d+numDirs*c;
// System.out.println("i="+i+", j="+j+", c="+c+", d="+d);
// saved values are PSF radius, convert to FWHM by multiplying by 2.0
double value=samples[i][j][c][d]*2.0;
// discard above threshold (in pixels, raw FWHM data)
if (Double.isNaN(value)) {
System.out.println("samples["+i+"]["+j+"]["+c+"]["+d+"] = Double.NaN, motors[0]="+ffm.motors[0]);
continue; // bad measurement
}
if (thresholdMax != null){
if (value >= thresholdMax[chn]) continue; // bad measurement (above threshold)
}
// correct for for minimal measurement;
if (minMeas != null){
if (value<minMeas[chn]) continue; // bad measurement (smaller than correction)
value=Math.sqrt(value*value-minMeas[chn]*minMeas[chn]);
}
// correct for for maximal measurement;
if (maxMeas != null) {
if (value >= maxMeas[chn]) continue; // bad measurement (larger than correction)
value = 1.0/Math.sqrt(1.0/(value*value)-1.0/(maxMeas[chn]*maxMeas[chn]));
if ((c<samples[i][j].length) && (samples[i][j][c]!=null)){
double sagTan[] = {
Math.sqrt(
cosSin2Tab[i][j][0]*samples[i][j][c][0]+
cosSin2Tab[i][j][1]*samples[i][j][c][1]+
cosSin2Tab[i][j][2]*samples[i][j][c][2]),
Math.sqrt(
cosSin2Tab[i][j][1]*samples[i][j][c][0]+
cosSin2Tab[i][j][0]*samples[i][j][c][1]-
cosSin2Tab[i][j][2]*samples[i][j][c][2])};
double sagTan_dx0[] = {
(0.5*(
cosSin2Tab_dx0[i][j][0]*samples[i][j][c][0]+
cosSin2Tab_dx0[i][j][1]*samples[i][j][c][1]+
cosSin2Tab_dx0[i][j][2]*samples[i][j][c][2])/sagTan[0]),
(0.5*(
cosSin2Tab_dx0[i][j][1]*samples[i][j][c][0]+
cosSin2Tab_dx0[i][j][0]*samples[i][j][c][1]-
cosSin2Tab_dx0[i][j][2]*samples[i][j][c][2])/sagTan[1])
};
double sagTan_dy0[] = {
(0.5*(
cosSin2Tab_dy0[i][j][0]*samples[i][j][c][0]+
cosSin2Tab_dy0[i][j][1]*samples[i][j][c][1]+
cosSin2Tab_dy0[i][j][2]*samples[i][j][c][2])/sagTan[0]),
(0.5*(
cosSin2Tab_dy0[i][j][1]*samples[i][j][c][0]+
cosSin2Tab_dy0[i][j][0]*samples[i][j][c][1]-
cosSin2Tab_dy0[i][j][2]*samples[i][j][c][2])/sagTan[1])
};
System.out.print("\n"+ffm.motors[2]+" i= "+i+" j= "+j+" c= "+c+" sagTan= "+sagTan[0]+" "+sagTan[1]+" ");
for (int d=0;d<numDirs;d++){
System.out.print(" d= "+d+" ");
if (!updateSelection && !sampleMask[i][j][c][d]) continue;
int chn=d+numDirs*c;
// System.out.println("i="+i+", j="+j+", c="+c+", d="+d);
// saved values are PSF radius, convert to FWHM by multiplying by 2.0
double value=sagTan[d]*2.0;
double value_dx0=sagTan_dx0[d]*2.0;
double value_dy0=sagTan_dy0[d]*2.0;
// discard above threshold (in pixels, raw FWHM data)
if (Double.isNaN(value)) {
System.out.println("samples["+i+"]["+j+"]["+c+"]["+d+"] = Double.NaN, motors[0]="+ffm.motors[0]);
continue; // bad measurement
}
System.out.print(" A "+value);
if (thresholdMax != null){
if (value >= thresholdMax[chn]) {
System.out.print(" > "+thresholdMax[chn]);
continue; // bad measurement (above threshold)
}
}
System.out.print(" B "+value);
// correct for for minimal measurement;
if (minMeas != null){
if (value<minMeas[chn]) continue; // bad measurement (smaller than correction)
double f=value;
value=Math.sqrt(value*value-minMeas[chn]*minMeas[chn]);
value_dx0*=f/value;
value_dy0*=f/value;
}
System.out.print(" C "+value);
// correct for for maximal measurement;
if (maxMeas != null) {
if (value >= maxMeas[chn]) continue; // bad measurement (larger than correction)
double f=value;
value = 1.0/Math.sqrt(1.0/(value*value)-1.0/(maxMeas[chn]*maxMeas[chn]));
value_dx0*=1.0/(value*f*f*f);
value_dy0*=1.0/(value*f*f*f);
}
System.out.print(" D "+value);
// convert to microns from pixels
value*=getPixelUM();
sampleList.add(new MeasuredSample(
ffm.motors,
ffm.timestamp,
sampleCoord[i][j][0], // px,
sampleCoord[i][j][1], // py,
chn,
value,
value_dx0, //double dPxc; // derivative of the value by optical (aberration) center pixel X
value_dy0 //double dPyc; // derivative of the value by optical (aberration) center pixel Y
));
System.out.print(" E "+value);
if (updateSelection) sampleMask[i][j][c][d]=true;
}
// convert to microns from pixels
value*=getPixelUM();
sampleList.add(new MeasuredSample(
ffm.motors,
ffm.timestamp,
sampleCoord[i][j][0], // px,
sampleCoord[i][j][1], // py,
chn,
value
));
}
}
}
}
}
}
System.out.println();
System.out.println("createDataVector -> "+sampleList.size()+" elements");
return sampleList.toArray(new MeasuredSample[0]);
}
......@@ -616,9 +822,9 @@ public class FocusingField {
// this.savedJacobian=this.jacobian;
this.savedLMAArrays=lMAArrays.clone();
this.jacobian=null; // not needed, just to catch bugs
this.nextfX=createFXandJacobian(this.nextVector,true);
this.lMAArrays=calculateJacobianArrays(this.nextfX);
this.nextRMS= calcErrorDiffY(this.nextfX);
this.nextfX=createFXandJacobian(this.nextVector,true);
this.lMAArrays=calculateJacobianArrays(this.nextfX);
this.nextRMS= calcErrorDiffY(this.nextfX);
this.lastImprovements[1]=this.lastImprovements[0];
this.lastImprovements[0]=this.currentRMS-this.nextRMS;
if (debugLevel>2) {
......@@ -832,6 +1038,21 @@ public class FocusingField {
for (int i=1;i<selChanIndices.length;i++){
selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0);
}
double [][][] cosSin2Tab=new double[sampleCoord.length][sampleCoord[0].length][3];
for (int i=0;i<sampleMask.length;i++) for (int j=0;j<sampleMask[i].length;j++){
double delta_x=sampleCoord[i][j][0]-currentPX0;
double delta_y=sampleCoord[i][j][1]-currentPY0;
double r2=delta_x*delta_x+delta_y*delta_y;
if (r2>0.0) {
cosSin2Tab[i][j][0]= delta_x*delta_x/r2; // cos^2
cosSin2Tab[i][j][1]= delta_y*delta_y/r2; // sin^2
cosSin2Tab[i][j][2]=2*delta_x*delta_y/r2; // 2*cos*sin
} else {
cosSin2Tab[i][j][0]=1.0;
cosSin2Tab[i][j][1]=0.0;
cosSin2Tab[i][j][2]=0.0;
}
}
StringBuffer sb = new StringBuffer();
if (showMotors) header +="M1\tM2\tM3\t";
......@@ -871,30 +1092,51 @@ public class FocusingField {
if (showMeasCalc[0] && (samples!=null)) for (int i=0;i<sampleCoord.length;i++){
if ((i<samples.length) && (samples[i]!=null)) for (int j=0;j<sampleCoord[i].length;j++){
if ((j<samples[i].length) && (samples[i][j]!=null)) for (int c=0;c<numColors;c++){
if ((c<samples[i][j].length) && (samples[i][j][c]!=null)) for (int d=0;d<numDirs;d++){
int chn=d+numDirs*c;
// System.out.println("i="+i+", j="+j+", c="+c+", d="+d);
// saved values are PSF radius, convert to FWHM by multiplying by 2.0
double value=samples[i][j][c][d]*2.0;
// discard above threshold (in pixels, raw FWHM data)
if (Double.isNaN(value)) continue; // bad measurement
if (!showIgnoredData && (thresholdMax != null)){
if (value >= thresholdMax[chn]) continue; // bad measurement (above threshold)
}
// correct for for minimal measurement;
if (useMinMeas && (minMeas != null)){
if (value<minMeas[chn]) continue; // bad measurement (smaller than correction)
value=Math.sqrt(value*value-minMeas[chn]*minMeas[chn]);
}
// correct for for maximal measurement;
if (useMaxMeas && (maxMeas != null)) {
if (value >= maxMeas[chn]) continue; // bad measurement (larger than correction)
value = 1.0/Math.sqrt(1.0/(value*value)-1.0/(maxMeas[chn]*maxMeas[chn]));
}
// convert to microns from pixels
value*=getPixelUM();
samplesFull[i][j][c][d]=value;
}
if ((c<samples[i][j].length) && (samples[i][j][c]!=null)) {
double sagTan[] = {
Math.sqrt(
cosSin2Tab[i][j][0]*samples[i][j][c][0]+
cosSin2Tab[i][j][1]*samples[i][j][c][1]+
cosSin2Tab[i][j][2]*samples[i][j][c][2]),
Math.sqrt(
cosSin2Tab[i][j][1]*samples[i][j][c][0]+
cosSin2Tab[i][j][0]*samples[i][j][c][1]-
cosSin2Tab[i][j][2]*samples[i][j][c][2])};
System.out.print("\n"+ffm.motors[2]+" i= "+i+" j= "+j+" c= "+c+" sagTan= "+sagTan[0]+" "+sagTan[1]+" ");
for (int d=0;d<numDirs;d++){
System.out.print(" d= "+d+" ");
int chn=d+numDirs*c;
// System.out.println("i="+i+", j="+j+", c="+c+", d="+d);
// saved values are PSF radius, convert to FWHM by multiplying by 2.0
double value=sagTan[d]*2.0;
// discard above threshold (in pixels, raw FWHM data)
if (Double.isNaN(value)) continue; // bad measurement
System.out.print(" A "+value);
if (!showIgnoredData && (thresholdMax != null)){
if (value >= thresholdMax[chn]){
System.out.print(" > "+thresholdMax[chn]);
continue; // bad measurement (above threshold)
}
}
System.out.print(" B "+value);
// correct for for minimal measurement;
if (useMinMeas && (minMeas != null)){
if (value<minMeas[chn]) continue; // bad measurement (smaller than correction)
value=Math.sqrt(value*value-minMeas[chn]*minMeas[chn]);
}
System.out.print(" C "+value);
// correct for for maximal measurement;
if (useMaxMeas && (maxMeas != null)) {
if (value >= maxMeas[chn]) continue; // bad measurement (larger than correction)
value = 1.0/Math.sqrt(1.0/(value*value)-1.0/(maxMeas[chn]*maxMeas[chn]));
}
System.out.print(" D "+value);
// convert to microns from pixels
value*=getPixelUM();
samplesFull[i][j][c][d]=value;
System.out.print(" E "+value);
}
}
}
}
}
......@@ -949,6 +1191,9 @@ public class FocusingField {
}
sb.append("\n");
}
System.out.println();
if (showRad){
sb.append(header+"\n");
if (showMotors) sb.append("Sample\tradius\t(mm)\t");
......@@ -1070,7 +1315,7 @@ public class FocusingField {
String msg="Calculation aborted by user request, restoring saved parameter vector";
IJ.showMessage(msg);
System.out.println(msg);
this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
commitParameterVector(this.savedVector);
return false;
}
......@@ -1121,13 +1366,13 @@ public class FocusingField {
// updateCameraParametersFromCalculated(false); // update camera parameters from enabled only images (may overwrite some of the above)
}
// if RMS was decreased. this.saveSeries==false after dialogLMAStep(state) only if "cancel" was pressed
this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster); // either new or original
commitParameterVector(this.savedVector); // either new or original
return this.saveSeries; // TODO: Maybe change result?
}
//stepLevenbergMarquardtAction();
if (state[1]) {
if (!state[0]) {
this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
commitParameterVector(this.savedVector);
return false; // sequence failed
}
this.savedVector=this.currentVector.clone();
......@@ -1147,7 +1392,7 @@ public class FocusingField {
" ("+this.firstRMS+") "+
" at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3));
this.savedVector=this.currentVector.clone();
this.fieldFitting.commitParameterVector(this.savedVector,sagittalMaster);
commitParameterVector(this.savedVector);
return true; // all series done
}
......@@ -1163,7 +1408,7 @@ public class FocusingField {
public String timestamp;
public double temperature;
public int [] motors;
double [][][][] samples = null;
double [][][][] samples = null; // last - psf radius in pixels: {x2,y2, xy}
public FocusingFieldMeasurement(
String timestamp,
......@@ -1176,16 +1421,21 @@ public class FocusingField {
this.motors = new int[motors.length];
for (int i=0;i<motors.length;i++) this.motors[i]= motors[i];
if (samples !=null) {
this.samples=new double[samples.length][samples[0].length][samples[0][0].length][2];
// this.samples=new double[samples.length][samples[0].length][samples[0][0].length][2];
try {
this.samples=new double[samples.length][samples[0].length][samples[0][0].length][3];
} catch (Exception e){
return;
}
for (int i=0;i<this.samples.length;i++) for (int j=0;j<this.samples[i].length;j++) for (int c=0;c<this.samples[i][j].length;c++){
try {
double rt=samples[i][j][c][0]/Math.sqrt((1+samples[i][j][c][1]*samples[i][j][c][1])/2.0); // tangential;
double rs=rt*samples[i][j][c][1]; // sagittal
this.samples[i][j][c][0]=rs;
this.samples[i][j][c][1]=rt;
// double rt=samples[i][j][c][0]/Math.sqrt((1+samples[i][j][c][1]*samples[i][j][c][1])/2.0); // tangential;
// double rs=rt*samples[i][j][c][1]; // sagittal
// this.samples[i][j][c][0]=rs;
// this.samples[i][j][c][1]=rt;
this.samples[i][j][c]=samples[i][j][c].clone();
} catch (Exception e){
this.samples[i][j][c][0]=Double.NaN;
this.samples[i][j][c][1]=Double.NaN;
for (int ii=0;ii<this.samples[i][j][c].length;ii++) this.samples[i][j][c][ii]=Double.NaN;
}
}
}
......@@ -1219,11 +1469,14 @@ public class FocusingField {
String [] ps=s.split(regSep);
int i=Integer.parseInt(ps[0]);
int j=Integer.parseInt(ps[1]);
int colors=(ps.length-2)/2;
this.samples[i][j]=new double [colors][2];
int colors=(ps.length-2)/3; // 2;
this.samples[i][j]=new double [colors][3]; //[2];
for (int c=0;c<colors;c++){
this.samples[i][j][c][0]=Double.parseDouble(ps[2*c+2]);
this.samples[i][j][c][1]=Double.parseDouble(ps[2*c+3]);
// this.samples[i][j][c][0]=Double.parseDouble(ps[2*c+2]);
// this.samples[i][j][c][1]=Double.parseDouble(ps[2*c+3]);
this.samples[i][j][c][0]=Double.parseDouble(ps[3*c+2]);
this.samples[i][j][c][1]=Double.parseDouble(ps[3*c+3]);
this.samples[i][j][c][2]=Double.parseDouble(ps[3*c+4]);
}
}
}
......@@ -1235,8 +1488,11 @@ public class FocusingField {
for (int i=0;i<this.samples.length;i++) for (int j=0;j<this.samples[i].length;j++){
String sdata=i+sep+j;
for (int c=0;c<samples[i][j].length;c++) {
sdata += sep+this.samples[i][j][c][0]+ // sagittal
sep+this.samples[i][j][c][1]; // tangential
// sdata += sep+this.samples[i][j][c][0]+ // sagittal
// sep+this.samples[i][j][c][1]; // tangential
sdata += sep+this.samples[i][j][c][0]+ // x2
sep+this.samples[i][j][c][1]+ // y2
sep+this.samples[i][j][c][2]; // xy
}
nodeList.add(sdata);
}
......@@ -1255,8 +1511,11 @@ public class FocusingField {
this.serialNumber=serialNumber;
this.lensSerial=lensSerial;
this.comment=comment;
this.pX0=pX0;
this.pY0=pY0;
this.pX0_distortions=pX0;
this.pY0_distortions=pY0;
// copy distortions to current PX0/PY0
this.currentPX0=pX0_distortions;
this.currentPY0=pY0_distortions;
this.sampleCoord=sampleCoord;
this.measurements=new ArrayList<FocusingFieldMeasurement>();
this.stopRequested=stopRequested;
......@@ -1306,8 +1565,11 @@ public class FocusingField {
comment= hConfig.getString("comment","no comments");
serialNumber= hConfig.getString("serialNumber","???");
lensSerial= hConfig.getString("lensSerial","???");
pX0=Double.parseDouble(hConfig.getString("lens_center_x","0.0"));
pY0=Double.parseDouble(hConfig.getString("lens_center_y","0.0"));
pX0_distortions=Double.parseDouble(hConfig.getString("lens_center_x","0.0"));
pY0_distortions=Double.parseDouble(hConfig.getString("lens_center_y","0.0"));
// copy distortions to current PX0/PY0
this.currentPX0=pX0_distortions;
this.currentPY0=pY0_distortions;
int rows=Integer.parseInt(hConfig.getString("samples_y","0"));
int cols=Integer.parseInt(hConfig.getString("samples_x","0"));
sampleCoord=new double [rows][cols][2];
......@@ -1342,8 +1604,8 @@ public class FocusingField {
if (comment!=null) hConfig.addProperty("comment",comment);
if (serialNumber!=null) hConfig.addProperty("serialNumber",serialNumber);
if (lensSerial!=null) hConfig.addProperty("lensSerial",lensSerial);
hConfig.addProperty("lens_center_x",pX0);
hConfig.addProperty("lens_center_y",pY0);
hConfig.addProperty("lens_center_x",pX0_distortions); // distortions center, not aberrations!
hConfig.addProperty("lens_center_y",pY0_distortions);
if ((sampleCoord!=null) && (sampleCoord.length>0) && (sampleCoord[0] != null) && (sampleCoord[0].length>0)){
hConfig.addProperty("samples_x",sampleCoord[0].length);
hConfig.addProperty("samples_y",sampleCoord.length);
......@@ -1376,6 +1638,9 @@ public class FocusingField {
}
}
public class FieldFitting{
public double [] pXY=null;
public boolean [] centerSelect=null;
public boolean [] centerSelectDefault={true,true};
MechanicalFocusingModel mechanicalFocusingModel;
CurvatureModel [] curvatureModel=new CurvatureModel[6]; // 3 colors, sagittal+tangential each
boolean [] channelSelect=null;
......@@ -1389,6 +1654,13 @@ public class FocusingField {
return channelDescriptions[i];
}
public boolean [] getCenterSelect(){
return centerSelect;
}
public double[] getCenterXY(){
return pXY;
}
public boolean[] getDefaultMask(){
boolean [] mask = {true,true,true,true,true,true};
return mask;
......@@ -1401,9 +1673,13 @@ public class FocusingField {
int distanceParametersNumber,
int radialParametersNumber)
{
pXY=new double [2];
pXY[0]=pX0;
pXY[1]=pY0;
channelSelect=getDefaultMask();
mechanicalFocusingModel=new MechanicalFocusingModel();
mechanicalSelect=mechanicalFocusingModel.getDefaultMask();
centerSelect=centerSelectDefault.clone();
for (int i=0;i<curvatureModel.length;i++){
curvatureModel[i]= new CurvatureModel(
pX0,
......@@ -1432,6 +1708,9 @@ public class FocusingField {
boolean editCurvMask=false;
boolean commonCurvMask=true;
boolean detailedCurvMask=false;
if (centerSelect==null) centerSelect=centerSelectDefault.clone();
gd.addCheckbox("Adjust aberration center (pX0)", centerSelect[0]);
gd.addCheckbox("Adjust aberration center (pY0)", centerSelect[1]);
if (channelSelect==null) channelSelect=getDefaultMask();
for (int i=0;i<channelSelect.length;i++) {
......@@ -1445,6 +1724,8 @@ public class FocusingField {
// gd.enableYesNoCancel("Keep","Apply"); // default OK (on enter) - "Keep"
gd.showDialog();
if (gd.wasCanceled()) return false;
centerSelect[0]=gd.getNextBoolean();
centerSelect[1]=gd.getNextBoolean();
for (int i=0;i<channelSelect.length;i++) {
channelSelect[i]=gd.getNextBoolean();
}
......@@ -1493,6 +1774,15 @@ public class FocusingField {
}
ArrayList<String> getParameterValueStrings(boolean showDisabled){
ArrayList<String> parList=new ArrayList<String>();
parList.add("\t ===== Aberrations center =====\t\t");
String [] centerDescriptions={"Aberrations center X","Aberrations center Y"};
for (int i=0;i<2;i++){
if (centerSelect[i] ) {
parList.add("\t"+centerDescriptions[i]+":\t"+pXY[i]+"\tpix");
} else if (showDisabled){
parList.add("(disabled)\t"+centerDescriptions[i]+":\t"+pXY[i]+"\tpix");
}
}
parList.add("\t ===== Mechanical model parameters =====\t\t");
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) {
......@@ -1535,6 +1825,16 @@ public class FocusingField {
// Show/modify all parameters in a single window.
public boolean showModifyParameterValues(String title, boolean showDisabled){
GenericDialog gd = new GenericDialog(title);
gd.addMessage("===== Aberrations center =====");
String [] centerDescriptions={"Aberrations center X","Aberrations center Y"};
for (int i=0;i<2;i++){
if (centerSelect[i] ) {
gd.addNumericField(centerDescriptions[i],pXY[i],5,10,"pix");
} else if (showDisabled){
gd.addNumericField("(disabled) "+centerDescriptions[i],pXY[i],5,10,"pix");
}
}
gd.addMessage("===== Mechanical model parameters =====");
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) {
......@@ -1575,6 +1875,11 @@ public class FocusingField {
gd.showDialog();
if (gd.wasCanceled()) return false;
if (!gd.wasOKed()) { // selected non-default "Apply"
for (int i=0;i<2;i++){
if (centerSelect[i] || showDisabled) {
pXY[i]=gd.getNextNumber();
}
}
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] || showDisabled) {
mechanicalFocusingModel.paramValues[i]=gd.getNextNumber();
......@@ -1594,10 +1899,13 @@ public class FocusingField {
}
/**
* @return number of selected parameters (including mechanical and each selected - up to 6 - curvature)
* @return number of selected parameters (including center, mechanical and each selected - up to 6 - curvature)
*/
public int getNumberOfParameters(boolean sagittalMaster){
int np=0;
for (int i=0;i<2;i++){
if ( centerSelect[i]) np++;
}
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) np++;
}
......@@ -1627,6 +1935,10 @@ public class FocusingField {
public double [] createParameterVector(boolean sagittalMaster){
double [] pars = new double [getNumberOfParameters(sagittalMaster)];
int np=0;
for (int i=0;i<2;i++){
if ( centerSelect[i]) pars[np++]=pXY[i];
}
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) pars[np++]=mechanicalFocusingModel.paramValues[i];
}
......@@ -1649,6 +1961,9 @@ public class FocusingField {
*/
public void commitParameterVector(double [] pars, boolean sagittalMaster){
int np=0;
for (int i=0;i<2;i++){
if ( centerSelect[i]) pXY[i]=pars[np++];
}
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) mechanicalFocusingModel.paramValues[i] = pars[np++];;
}
......@@ -1669,9 +1984,11 @@ public class FocusingField {
if (isMasterDir){
curvatureModel[n ^ 1].setCenterVector(curvatureModel[n].getCenterVector());
}
}
}
// propagate pXY to each channel (even disabled)
for (int n=0;n<curvatureModel.length;n++){
curvatureModel[n].setCenter(pXY[0],pXY[1]);
}
}
public double getMotorsZ(
int [] motors, // 3 motor coordinates
......@@ -1687,10 +2004,17 @@ public class FocusingField {
public double getRadiusMM(
double px, // pixel x
double py) {// pixel y
double pd=Math.sqrt((px-pX0)*(px-pX0)+(py-pY0)*(py-pY0));
double pd=Math.sqrt((px-currentPX0)*(px-currentPX0)+(py-currentPY0)*(py-currentPY0));
return pd*getPixelMM();
}
public double getRadiusMM_distortions(
double px, // pixel x
double py) {// pixel y
double pd=Math.sqrt((px-pX0_distortions)*(px-pX0_distortions)+(py-pY0_distortions)*(py-pY0_distortions));
return pd*getPixelMM();
}
/**
* Generate vector of function values (up to 6 - 1 per selected channel), corresponding to motor positions and pixel
* coordinates, optionally generate partial derivatives for each channel and parameter
......@@ -1727,14 +2051,29 @@ public class FocusingField {
deriv_curv[c]);
}
if (deriv!=null){
double dX=px-pXY[0];
double dY=py-pXY[1];
double r=Math.sqrt(dX*dX+dY*dY);
double [] dr_dxy={1.0,1.0};
if (r>0.0){
dr_dxy[0]=-dX/r;
dr_dxy[1]=-dY/r;
}
nChn=0;
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
boolean isMasterDir=(c%2) == (sagittalMaster?0:1);
int otherChannel= c ^ 1;
deriv[nChn]=new double [getNumberOfParameters(sagittalMaster)];
int np=0;
for (int i=0;i<2;i++){
if (centerSelect[i] ) {
deriv[nChn][np++]=dr_dxy[i]*deriv_curv[c][deriv_curv[c].length-1]; // needs correction from measurement conversion
}
}
// For dependent/master channels no difference for mechanical parameters
// TOSO: verify they are the same?
// TODO: verify they are the same?
// calculate derivatives for the center variations (/dXc, /dYc). Will need to be modified for Y vector too as
// Y-vector two values (S,T) are calculated from 3 (X2,Y2,XY) and depend on the center position.
for (int i=0;i<mechanicalFocusingModel.paramValues.length;i++){
if ((mechanicalSelect==null) || mechanicalSelect[i] ) {
......@@ -2071,9 +2410,9 @@ public class FocusingField {
private double dflt_na=0.15; // um/um
private double dflt_r0=4.0; //3.3; // um (1.5 pix)
private double [][] modelParams=null;
public static final int dflt_distanceParametersNumber=4;
public static final int dflt_distanceParametersNumber=5;
public static final int dflt_radialParametersNumber=3;
private static final int min_distanceParametersNumber=3;
private static final int min_distanceParametersNumber=4;
private static final int min_radialParametersNumber=1;
private double pX0,pY0;
public CurvatureModel(
......@@ -2088,6 +2427,10 @@ public class FocusingField {
this.modelParams=new double [distanceParametersNumber][radialParametersNumber];
setDefaults();
}
public void setCenter(double pX, double pY){
pX0=pX;
pY0=pY;
}
public int [] getNumPars(){
if (modelParams==null) return null;
int [] numPars={modelParams.length,modelParams[0].length};
......@@ -2129,7 +2472,7 @@ public class FocusingField {
}
public int getSize(){
try {
return this.modelParams.length*this.modelParams[0].length;
return this.modelParams.length*this.modelParams[0].length+1; // last element df/dr
} catch (Exception e){
return 0;
}
......@@ -2142,7 +2485,7 @@ public class FocusingField {
* @param pX - sample pixel x coordinate (currently just for radius calculation)
* @param pY - sample pixel y coordinate (currently just for radius calculation)
* @param z_in - z (from mechanical) before subtracting of z0
* @param deriv array to accommodate all partial derivatives or null
* @param deriv array to accommodate all partial derivatives or null (should have modelParams.length*modelParams[0].length+1
* @return function value
*/
public double getFdF(
......@@ -2167,13 +2510,15 @@ ar1 - ar[4]
*/
double r=Math.sqrt((pX-pX0)*(pX-pX0)+(pY-pY0)*(pY-pY0))*PIXEL_SIZE; // in mm
double r2=r*r;
// double r2=r*r;
double [] ar= new double [this.modelParams.length];
for (int i=0;i<this.modelParams.length;i++){
ar[i]=this.modelParams[i][0];
double rp=1.0;
// double rp=1.0;
double rp=r;
for (int j=1;j<this.modelParams[i].length;j++){
rp*=r2;
// rp*=r2;
rp*=r;
ar[i]+=this.modelParams[i][j]*rp;
}
}
......@@ -2231,20 +2576,34 @@ 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]*r2;
dar[j]=dar[j-1]*r;
if (j==1) dar[j]*=r; // 0,2,3,4,5...
}
int index=0;
for (int i=0;i<this.modelParams.length;i++) for (int j=0;j<this.modelParams[0].length;j++){
deriv[index++]=df_da[i]*dar[j];
}
// calculate d(f)/d(r)
double df_dr=0.0;
for (int i=0;i<this.modelParams.length;i++){
double da_dr=0.0;
double rp=1.0;
for (int j=1; j<this.modelParams[0].length;j++) {
rp*=r;
da_dr+=this.modelParams[i][j]*(j+1)*rp;
}
df_dr+=df_da[i]*da_dr;
}
deriv[this.modelParams.length*this.modelParams[0].length]=df_dr; // last element
return f; // function value
}
public String getRadialName(int i){
return "ar_"+(2*i);
return "ar_"+(i+1);
}
public String getRadialDecription(int i){
if (i==0) return "Radial constant coefficient";
return "Radial polynomial coefficient for r^"+(2*i);
return "Radial polynomial coefficient for r^"+(i+1);
}
public String getZName(int i){
if (i==0) return "z0";
......
src/main/java/MatchSimulatedPattern.java
View file @ 57f9aca9
......@@ -5354,6 +5354,53 @@ java.lang.ArrayIndexOutOfBoundsException: -3566
return result;
}
//====================================================
public double [] x2y2xySizes(
double [] psf, // PSF function, square array, nominally positive
double cutoffEnergy, // fraction of energy in the pixels to be used
double cutoffLevel, // minimal level as a fraction of maximal
int minArea, // minimal selected area in pixels
double blurSigma, // optionally blur the selection
double maskCutOff,
int debugLevel, // debug level
String title) { // prefix used for debug images
double [] mask=findClusterOnPSF(
psf,
cutoffEnergy,
cutoffLevel,
minArea,
blurSigma,
debugLevel,
title);
for (int i=0;i<mask.length;i++)
if (mask[i]<maskCutOff) mask[i]=0.0;
int size = (int) Math.sqrt(psf.length);
int hsize=size/2;
// int nn=0;
double S0=0.0, SX=0.0, SY=0.0,SX2=0.0,SY2=0.0,SXY=0.0;
for (int i=0;i<mask.length;i++) if (mask[i]>0.0) {
double x=(i % size) - hsize;
double y=(i / size) - hsize;
double d=psf[i]*mask[i];
S0+=d;
SX+=d*x;
SY+=d*y;
SX2+=d*x*x;
SY2+=d*y*y;
SXY+=d*x*y;
// nn++;
}
if (S0==0.0) return null; // make sure it is OK
double [] result={
(SX2*S0 - SX*SX)/S0/S0,
(SY2*S0 - SY*SY)/S0/S0,
(SXY*S0 - SX*SY)/S0/S0}; // this may be negative
// System.out.println(" mask.length="+mask.length+" nn="+nn+" S0="+S0+" SX="+SX+" SY="+SY+" SX2="+SXR2+" SY2="+SY2+" SXY="+SXY+
// " result={"+result[0]+","+result[1]+","+result[2]+"}");
return result;
}
//====================================================
public double [] findClusterOnPSF(
......@@ -8509,6 +8556,7 @@ d()/dy=C*x+2*B*y+E=0
IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg);
}
if (this.PATTERN_GRID.length==0) return null;
double x1=x0,y1=y0;
double x2=x1+size;
double y2=y1+size;
......
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