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imagej-elphel
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
This diff is collapsed.
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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