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Commit 7d08fe37 authored by Andrey Filippov's avatar Andrey Filippov
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Added absoulte center option, debugging missing of the grid

parent 93c3e515
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Showing with 52 additions and 31 deletions
src/main/java/Aberration_Calibration.java
View file @ 7d08fe37
...@@ -143,6 +143,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene ...@@ -143,6 +143,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene
true, // useWindow - multiply separated OTF instance by window function (Hamming or Gaussian) true, // useWindow - multiply separated OTF instance by window function (Hamming or Gaussian)
false, // symm180 - force PSF center-symmetrical (around centroid that is defined by lateral chromatic aberration false, // symm180 - force PSF center-symmetrical (around centroid that is defined by lateral chromatic aberration
false, // ignoreChromatic - ignore lateral chromatic aberration (center PSF to 0,0) false, // ignoreChromatic - ignore lateral chromatic aberration (center PSF to 0,0)
true, // absoluteCenter - do not remove green correlation shift (forces ignoreChromatic=false)
0.2, // smoothSeparate - low pass filter width when separating individual PSF instances 0.2, // smoothSeparate - low pass filter width when separating individual PSF instances
0.75, // topCenter - consider only points above this fraction of the peak to find the centroid 0.75, // topCenter - consider only points above this fraction of the peak to find the centroid
0.0, // sigmaToRadius - variable-sigma blurring to reduce high frequencies more for the pixels farther from the PSF center 0.0, // sigmaToRadius - variable-sigma blurring to reduce high frequencies more for the pixels farther from the PSF center
...@@ -16998,7 +16999,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //********************************************* ...@@ -16998,7 +16999,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //*********************************************
kernels[i]=combinePSF (inverted[i], // Square array of pixels with multiple repeated PSF (alternating sign) kernels[i]=combinePSF (inverted[i], // Square array of pixels with multiple repeated PSF (alternating sign)
true, // master, force ignoreChromatic !psfParameters.absoluteCenter, //true, // master, force ignoreChromatic
PSF_shifts[i], // centerXY[] - will be modified inside combinePSF() if PSF_PARS.ignoreChromatic is true PSF_shifts[i], // centerXY[] - will be modified inside combinePSF() if PSF_PARS.ignoreChromatic is true
PSF_centroids[i], // will return array of XY coordinates of the result centroid PSF_centroids[i], // will return array of XY coordinates of the result centroid
(i==4)?wVectors4:wVectors, // two wave vectors, lengths in cycles/pixel (pixels match pixel array) (i==4)?wVectors4:wVectors, // two wave vectors, lengths in cycles/pixel (pixels match pixel array)
...@@ -17009,7 +17010,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //********************************************* ...@@ -17009,7 +17010,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //*********************************************
if (DEBUG_LEVEL>2) System.out.println("After-1: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts [i][0],3)+" PSF_shifts["+i+"][1]="+IJ.d2s( PSF_shifts[i][1],3)); if (DEBUG_LEVEL>2) System.out.println("After-1: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts [i][0],3)+" PSF_shifts["+i+"][1]="+IJ.d2s( PSF_shifts[i][1],3));
if (DEBUG_LEVEL>2) System.out.println("After-1: color Component "+i+" PSF_centroids["+i+"][0]="+IJ.d2s(PSF_centroids[i][0],3)+" PSF_centroids["+i+"][1]="+IJ.d2s(PSF_centroids[i][1],3)); if (DEBUG_LEVEL>2) System.out.println("After-1: color Component "+i+" PSF_centroids["+i+"][0]="+IJ.d2s(PSF_centroids[i][0],3)+" PSF_centroids["+i+"][1]="+IJ.d2s(PSF_centroids[i][1],3));
if (!psfParameters.ignoreChromatic) { /* Recalculate center to pixels from greens (diagonal)) and supply it to other colors (lateral chromatic aberration correction) */ if (!psfParameters.ignoreChromatic && !psfParameters.absoluteCenter) { /* Recalculate center to pixels from greens (diagonal)) and supply it to other colors (lateral chromatic aberration correction) */
for (j=0;j<input_bayer.length;j++) if ((colorComponents.colorsToCorrect[j]) && (j!=referenceComp)) { for (j=0;j<input_bayer.length;j++) if ((colorComponents.colorsToCorrect[j]) && (j!=referenceComp)) {
PSF_shifts[j]=shiftSensorToBayer (shiftBayerToSensor(PSF_shifts[referenceComp],referenceComp,subpixel),j,subpixel); PSF_shifts[j]=shiftSensorToBayer (shiftBayerToSensor(PSF_shifts[referenceComp],referenceComp,subpixel),j,subpixel);
if (DEBUG_LEVEL>2) System.out.println("After-2 (recalc): color Component "+j+" PSF_shifts["+j+"][0]="+IJ.d2s(PSF_shifts[j][0],3)+" PSF_shifts["+j+"][1]="+IJ.d2s(PSF_shifts[j][1],3)); if (DEBUG_LEVEL>2) System.out.println("After-2 (recalc): color Component "+j+" PSF_shifts["+j+"][0]="+IJ.d2s(PSF_shifts[j][0],3)+" PSF_shifts["+j+"][1]="+IJ.d2s(PSF_shifts[j][1],3));
...@@ -17052,6 +17053,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //********************************************* ...@@ -17052,6 +17053,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //*********************************************
if (DEBUG_LEVEL>2) { //2 if (DEBUG_LEVEL>2) { //2
System.out.println("Color Component "+i+" subpixel="+subpixel+ System.out.println("Color Component "+i+" subpixel="+subpixel+
" psfParameters.ignoreChromatic="+psfParameters.ignoreChromatic+ " psfParameters.ignoreChromatic="+psfParameters.ignoreChromatic+
" psfParameters.absoluteCenter="+psfParameters.absoluteCenter+
" psfParameters.symm180="+psfParameters.symm180); " psfParameters.symm180="+psfParameters.symm180);
System.out.println( " PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+ System.out.println( " PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+
" PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3)+ " PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3)+
...@@ -17458,7 +17460,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //********************************************* ...@@ -17458,7 +17460,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //*********************************************
debug); debug);
// true); // true);
if (!master && !psfParameters.ignoreChromatic && psfParameters.centerPSF && (centerXY!=null)){ if (!master && !psfParameters.ignoreChromatic && !psfParameters.absoluteCenter && psfParameters.centerPSF && (centerXY!=null)){
// System.out.println("1:pixelsPSF.length="+pixelsPSF.length+" outSize+"+outSize); // System.out.println("1:pixelsPSF.length="+pixelsPSF.length+" outSize+"+outSize);
// TODO: Shift +/- 0.5 Pix here {centerXY[0]-Math.round(centerXY[0]),centerXY[1]-Math.round(centerXY[1])} // TODO: Shift +/- 0.5 Pix here {centerXY[0]-Math.round(centerXY[0]),centerXY[1]-Math.round(centerXY[1])}
...@@ -17515,7 +17517,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //********************************************* ...@@ -17515,7 +17517,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //*********************************************
if (DEBUG_LEVEL>2) System.out.println("Centroid after first binPSF: x="+IJ.d2s(centroidXY[0],3)+" y="+IJ.d2s(centroidXY[1],3)+" center was at x="+IJ.d2s(centerXY[0],3)+" y="+IJ.d2s(centerXY[1],3)); if (DEBUG_LEVEL>2) System.out.println("Centroid after first binPSF: x="+IJ.d2s(centroidXY[0],3)+" y="+IJ.d2s(centroidXY[1],3)+" center was at x="+IJ.d2s(centerXY[0],3)+" y="+IJ.d2s(centerXY[1],3));
/* Re-bin results with the new center if ignoreChromatic is true, update centerXY[](shift of the result PSF array) and centroidXY[] (center of the optionally shifted PDF array) */ /* Re-bin results with the new center if ignoreChromatic is true, update centerXY[](shift of the result PSF array) and centroidXY[] (center of the optionally shifted PDF array) */
if (master || psfParameters.ignoreChromatic) { if (!psfParameters.absoluteCenter && (master || psfParameters.ignoreChromatic)) {
if (centerXY!=null) { if (centerXY!=null) {
centerXY[0]+=centroidXY[0]; centerXY[0]+=centroidXY[0];
centerXY[1]+=centroidXY[1]; centerXY[1]+=centroidXY[1];
...@@ -18936,6 +18938,9 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica ...@@ -18936,6 +18938,9 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
gd.addCheckbox ("Multiply PSF cell by Hamming window", psfParameters.useWindow); // true; gd.addCheckbox ("Multiply PSF cell by Hamming window", psfParameters.useWindow); // true;
gd.addCheckbox ("Force PSF center- symmetrical (around centroid)", psfParameters.symm180); // true; // make OTF center-symmetrical (around centroid that is defined by lateral chromatic aberration) gd.addCheckbox ("Force PSF center- symmetrical (around centroid)", psfParameters.symm180); // true; // make OTF center-symmetrical (around centroid that is defined by lateral chromatic aberration)
gd.addCheckbox ("Ignore lateral chromatic aberrations, center PSF", psfParameters.ignoreChromatic); // true; // ignore lateral chromatic aberration (center OTF to 0,0) gd.addCheckbox ("Ignore lateral chromatic aberrations, center PSF", psfParameters.ignoreChromatic); // true; // ignore lateral chromatic aberration (center OTF to 0,0)
gd.addCheckbox ("Use absolute PSF center (no adjustment to green center)", psfParameters.absoluteCenter);
gd.addNumericField("PSF separation: low-pass filter width (to PSF half-period) ", psfParameters.smoothSeparate, 3); // 0.125 low pass filter width (relative to PSF pitch) when separation individual PSF gd.addNumericField("PSF separation: low-pass filter width (to PSF half-period) ", psfParameters.smoothSeparate, 3); // 0.125 low pass filter width (relative to PSF pitch) when separation individual PSF
gd.addNumericField("PSF separation: threshold to find the PSF maximum", psfParameters.topCenter, 3); // 0.75 consider only points above this fraction of the peak to find the centroid gd.addNumericField("PSF separation: threshold to find the PSF maximum", psfParameters.topCenter, 3); // 0.75 consider only points above this fraction of the peak to find the centroid
gd.addNumericField("PSF variable Gauss blurring (farther from center, higher the sigma", psfParameters.sigmaToRadius,3); // 0.4 variable-sigma blurring to reduce high frequencies more for the pixels farther from the PSF center gd.addNumericField("PSF variable Gauss blurring (farther from center, higher the sigma", psfParameters.sigmaToRadius,3); // 0.4 variable-sigma blurring to reduce high frequencies more for the pixels farther from the PSF center
...@@ -18958,6 +18963,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica ...@@ -18958,6 +18963,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
psfParameters.useWindow= gd.getNextBoolean(); psfParameters.useWindow= gd.getNextBoolean();
psfParameters.symm180= gd.getNextBoolean(); psfParameters.symm180= gd.getNextBoolean();
psfParameters.ignoreChromatic= gd.getNextBoolean(); psfParameters.ignoreChromatic= gd.getNextBoolean();
psfParameters.absoluteCenter= gd.getNextBoolean();
psfParameters.smoothSeparate= gd.getNextNumber(); psfParameters.smoothSeparate= gd.getNextNumber();
psfParameters.topCenter= gd.getNextNumber(); psfParameters.topCenter= gd.getNextNumber();
psfParameters.sigmaToRadius= gd.getNextNumber(); psfParameters.sigmaToRadius= gd.getNextNumber();
...@@ -19680,6 +19686,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica ...@@ -19680,6 +19686,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
gd.addNumericField("PSF wings energy (searching for ellipse approximation)", psfParameters.wingsEnergy, 3); // 0.8 fraction of energy in the pixels to be used gd.addNumericField("PSF wings energy (searching for ellipse approximation)", psfParameters.wingsEnergy, 3); // 0.8 fraction of energy in the pixels to be used
gd.addNumericField("PSF wings ellipse scale (multiply PSF by elliptical gaussian)",psfParameters.wingsEllipseScale, 3);// 2.0 increase wings cutoff ellipse by this from one defined by the cutoff energy gd.addNumericField("PSF wings ellipse scale (multiply PSF by elliptical gaussian)",psfParameters.wingsEllipseScale, 3);// 2.0 increase wings cutoff ellipse by this from one defined by the cutoff energy
gd.addCheckbox ("Ignore lateral chromatic aberrations, center PSF", psfParameters.ignoreChromatic); // true; // ignore lateral chromatic aberration (center OTF to 0,0) gd.addCheckbox ("Ignore lateral chromatic aberrations, center PSF", psfParameters.ignoreChromatic); // true; // ignore lateral chromatic aberration (center OTF to 0,0)
gd.addCheckbox ("Use absolute PSF center (no adjustment to green center)", psfParameters.absoluteCenter);
gd.addNumericField("OTF cutoff energy (used to determine bounding ellipse)", inverseParameters.otfCutoffEnergy, 3); //0.6; use frequency points that have inverseParameters.otfCutoffEnergy of the total to determine ellipse for limiting frequency responce gd.addNumericField("OTF cutoff energy (used to determine bounding ellipse)", inverseParameters.otfCutoffEnergy, 3); //0.6; use frequency points that have inverseParameters.otfCutoffEnergy of the total to determine ellipse for limiting frequency responce
gd.addNumericField("OTF size of elliptical window relative to cluster size", inverseParameters.otfEllipseScale, 3); //1.5; // size of elliptical window relative to the cluster defined by inverseParameters.otfCutoffEnergy gd.addNumericField("OTF size of elliptical window relative to cluster size", inverseParameters.otfEllipseScale, 3); //1.5; // size of elliptical window relative to the cluster defined by inverseParameters.otfCutoffEnergy
...@@ -19713,6 +19720,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica ...@@ -19713,6 +19720,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
psfParameters.wingsEnergy= gd.getNextNumber(); psfParameters.wingsEnergy= gd.getNextNumber();
psfParameters.wingsEllipseScale= gd.getNextNumber(); psfParameters.wingsEllipseScale= gd.getNextNumber();
psfParameters.ignoreChromatic= gd.getNextBoolean(); psfParameters.ignoreChromatic= gd.getNextBoolean();
psfParameters.absoluteCenter= gd.getNextBoolean();
inverseParameters.otfCutoffEnergy= gd.getNextNumber(); inverseParameters.otfCutoffEnergy= gd.getNextNumber();
inverseParameters.otfEllipseScale= gd.getNextNumber(); inverseParameters.otfEllipseScale= gd.getNextNumber();
inverseParameters.otfEllipseGauss= gd.getNextBoolean(); inverseParameters.otfEllipseGauss= gd.getNextBoolean();
......
src/main/java/Distortions.java
View file @ 7d08fe37
...@@ -3060,8 +3060,9 @@ For each point in the image ...@@ -3060,8 +3060,9 @@ For each point in the image
cell[0], //double px, cell[0], //double px,
cell[1]); //double py) cell[1]); //double py)
cell[0]+=corrXYARGB[0]; // measured-> corrected : subtract, projected->simulated:add; cell[0]+=corrXYARGB[0]; // measured-> corrected : subtract, projected->simulated:add;
cell[1]+=corrXYARGB[1]; cell[1]+=corrXYARGB[1]+0.0; // Debugging by adding +1.0!!
} }
// System.out.println("================== Added +0.0 to pixel y for debugging purposes! =====================");
return true; return true;
} }
src/main/java/EyesisAberrations.java
View file @ 7d08fe37
...@@ -1446,7 +1446,7 @@ public class EyesisAberrations { ...@@ -1446,7 +1446,7 @@ public class EyesisAberrations {
int globalDebugLevel int globalDebugLevel
){ ){
double [][][][] psfKernelMap; // will be lost - do we need it outside double [][][][] psfKernelMap; // will be lost - do we need it outside
double [][][][][] kernelsElllipsePars = new double[filenames.length][][][][]; double [][][][][] kernelsElllipsePars = new double[filenames.length][][][][]; //x0,y0,a,b,c,area
if (thisDebugLevel>0){ if (thisDebugLevel>0){
System.out.println("combinePSFKernels(): filenames.length="+filenames.length); System.out.println("combinePSFKernels(): filenames.length="+filenames.length);
} }
...@@ -1503,15 +1503,15 @@ public class EyesisAberrations { ...@@ -1503,15 +1503,15 @@ public class EyesisAberrations {
// System.out.println("nChn="+nChn+" nFile="+nFile+" tileY="+tileY+" tileX="+tileX); // System.out.println("nChn="+nChn+" nFile="+nFile+" tileY="+tileY+" tileX="+tileX);
if (kernelsElllipsePars[nFile][tileY][tileX][chn]!=null) { if (kernelsElllipsePars[nFile][tileY][tileX][chn]!=null) {
channels[chn]=true; channels[chn]=true;
c[0][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][0]; c[0][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][0]; // x0
c[1][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][1]; c[1][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][1]; // y0
c[2][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][2]; c[2][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][2]; // a
c[3][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][3]; c[3][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][3]; // b
c[4][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][4]; c[4][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][4]; // c
a=1/Math.sqrt(kernelsElllipsePars[nFile][tileY][tileX][chn][2]*kernelsElllipsePars[nFile][tileY][tileX][chn][3]- a=1/Math.sqrt(kernelsElllipsePars[nFile][tileY][tileX][chn][2]*kernelsElllipsePars[nFile][tileY][tileX][chn][3]-
kernelsElllipsePars[nFile][tileY][tileX][chn][4]*kernelsElllipsePars[nFile][tileY][tileX][chn][4]/4); kernelsElllipsePars[nFile][tileY][tileX][chn][4]*kernelsElllipsePars[nFile][tileY][tileX][chn][4]/4);
c[5][chn][nFile+1][tileY*kWidth+tileX]= Math.sqrt(a); // radius c[5][chn][nFile+1][tileY*kWidth+tileX]= Math.sqrt(a); // radius
c[6][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][5]; c[6][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][5]; // area
} else { } else {
c[0][chn][nFile+1][tileY*kWidth+tileX]=Double.NaN; c[0][chn][nFile+1][tileY*kWidth+tileX]=Double.NaN;
...@@ -2057,7 +2057,8 @@ public class EyesisAberrations { ...@@ -2057,7 +2057,8 @@ public class EyesisAberrations {
"", "",
debugLevel); debugLevel);
// ellipseCoeffs[tileY][tileX][chn]=findEllipseOnPSF(kernel, selection, ""); // ellipseCoeffs[tileY][tileX][chn]=findEllipseOnPSF(kernel, selection, "");
ec=findEllipseOnPSF(kernel, selection, "", debugLevel); ec=findEllipseOnPSF(kernel, selection, "", debugLevel); // x0,y0,a,b,c (r2= a* x^2*+b*y^2+c*x*y)
l=ec.length; l=ec.length;
ellipseCoeffs[tileY][tileX][chn]=new double[l+1]; ellipseCoeffs[tileY][tileX][chn]=new double[l+1];
for (i=0;i<ec.length;i++) ellipseCoeffs[tileY][tileX][chn][i]=ec[i]; for (i=0;i<ec.length;i++) ellipseCoeffs[tileY][tileX][chn][i]=ec[i];
...@@ -2776,6 +2777,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -2776,6 +2777,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
globalDebugLevel, globalDebugLevel,
title+"-"+i); title+"-"+i);
} }
int debugThreshold=1;
if (debugThis) SDFA_INSTANCE.showArrays(inverted, fft_size*subpixel, fft_size*subpixel, title+"_Combined-PSF"); if (debugThis) SDFA_INSTANCE.showArrays(inverted, fft_size*subpixel, fft_size*subpixel, title+"_Combined-PSF");
/* correct composite greens */ /* correct composite greens */
/* Here we divide wave vectors by subpixel as the pixels are already added */ /* Here we divide wave vectors by subpixel as the pixels are already added */
...@@ -2811,7 +2813,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -2811,7 +2813,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
//int [][] clusterMask; //int [][] clusterMask;
/* Start with referenceComp */ /* Start with referenceComp */
i= referenceComp; i= referenceComp;
if (globalDebugLevel>2) { if (globalDebugLevel>debugThreshold) {
System.out.println(x0+":"+y0+"1-PSF_shifts.length= "+PSF_shifts.length+" i="+i+" input_bayer.length="+input_bayer.length); System.out.println(x0+":"+y0+"1-PSF_shifts.length= "+PSF_shifts.length+" i="+i+" input_bayer.length="+input_bayer.length);
System.out.println("Before: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+ System.out.println("Before: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+
" PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3)); " PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3));
...@@ -2819,7 +2821,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -2819,7 +2821,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
kernels[i]=combinePSF (inverted[i], // Square array of pixels with multiple repeated PSF (alternating sign) kernels[i]=combinePSF (inverted[i], // Square array of pixels with multiple repeated PSF (alternating sign)
true, // master, force ignoreChromatic !psfParameters.absoluteCenter, //true, // master, force ignoreChromatic
PSF_shifts[i], // centerXY[] - will be modified inside combinePSF() if PSF_PARS.ignoreChromatic is true PSF_shifts[i], // centerXY[] - will be modified inside combinePSF() if PSF_PARS.ignoreChromatic is true
PSF_centroids[i], // will return array of XY coordinates of the result centroid PSF_centroids[i], // will return array of XY coordinates of the result centroid
(i==4)?wVectors4:wVectors, // two wave vectors, lengths in cycles/pixel (pixels match pixel array) (i==4)?wVectors4:wVectors, // two wave vectors, lengths in cycles/pixel (pixels match pixel array)
...@@ -2829,13 +2831,13 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -2829,13 +2831,13 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
(globalDebugLevel>4), (globalDebugLevel>4),
globalDebugLevel globalDebugLevel
); );
if (globalDebugLevel>2) System.out.println(x0+":"+y0+"After-1: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts [i][0],3)+" PSF_shifts["+i+"][1]="+IJ.d2s( PSF_shifts[i][1],3)); if (globalDebugLevel>debugThreshold) System.out.println(x0+":"+y0+"After-1: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts [i][0],3)+" PSF_shifts["+i+"][1]="+IJ.d2s( PSF_shifts[i][1],3));
if (globalDebugLevel>2) System.out.println(x0+":"+y0+"After-1: color Component "+i+" PSF_centroids["+i+"][0]="+IJ.d2s(PSF_centroids[i][0],3)+" PSF_centroids["+i+"][1]="+IJ.d2s(PSF_centroids[i][1],3)); if (globalDebugLevel>debugThreshold) System.out.println(x0+":"+y0+"After-1: color Component "+i+" PSF_centroids["+i+"][0]="+IJ.d2s(PSF_centroids[i][0],3)+" PSF_centroids["+i+"][1]="+IJ.d2s(PSF_centroids[i][1],3));
if (!psfParameters.ignoreChromatic) { /* Recalculate center to pixels from greens (diagonal)) and supply it to other colors (lateral chromatic aberration correction) */ if (!psfParameters.ignoreChromatic && !psfParameters.absoluteCenter) { /* Recalculate center to pixels from greens (diagonal)) and supply it to other colors (lateral chromatic aberration correction) */
for (j=0;j<input_bayer.length;j++) if ((colorComponents.colorsToCorrect[j]) && (j!=referenceComp)) { for (j=0;j<input_bayer.length;j++) if ((colorComponents.colorsToCorrect[j]) && (j!=referenceComp)) {
PSF_shifts[j]=shiftSensorToBayer (shiftBayerToSensor(PSF_shifts[referenceComp],referenceComp,subpixel),j,subpixel); PSF_shifts[j]=shiftSensorToBayer (shiftBayerToSensor(PSF_shifts[referenceComp],referenceComp,subpixel),j,subpixel);
if (globalDebugLevel>2) System.out.println(x0+":"+y0+"After-2 (recalc): color Component "+j+" PSF_shifts["+j+"][0]="+IJ.d2s(PSF_shifts[j][0],3)+" PSF_shifts["+j+"][1]="+IJ.d2s(PSF_shifts[j][1],3)); if (globalDebugLevel>debugThreshold) System.out.println(x0+":"+y0+"After-2 (recalc): color Component "+j+" PSF_shifts["+j+"][0]="+IJ.d2s(PSF_shifts[j][0],3)+" PSF_shifts["+j+"][1]="+IJ.d2s(PSF_shifts[j][1],3));
} }
} }
...@@ -2846,7 +2848,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -2846,7 +2848,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
lateralChromaticAbs[i]=Math.sqrt(lateralChromatic[i][0]*lateralChromatic[i][0]+lateralChromatic[i][1]*lateralChromatic[i][1]); lateralChromaticAbs[i]=Math.sqrt(lateralChromatic[i][0]*lateralChromatic[i][0]+lateralChromatic[i][1]*lateralChromatic[i][1]);
/* Now process all the other components */ /* Now process all the other components */
for (i=0; i<input_bayer.length;i++) if ((i!=referenceComp) && (colorComponents.colorsToCorrect[i])) { for (i=0; i<input_bayer.length;i++) if ((i!=referenceComp) && (colorComponents.colorsToCorrect[i])) {
if (globalDebugLevel>2) { if (globalDebugLevel>debugThreshold) {
System.out.println(x0+":"+y0+"2-PSF_shifts.length= "+PSF_shifts.length+" i="+i+" input_bayer.length="+input_bayer.length); System.out.println(x0+":"+y0+"2-PSF_shifts.length= "+PSF_shifts.length+" i="+i+" input_bayer.length="+input_bayer.length);
System.out.println(x0+":"+y0+"Before: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+ System.out.println(x0+":"+y0+"Before: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+
...@@ -2862,8 +2864,8 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -2862,8 +2864,8 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
title+"_"+i, // reduce the PSF cell size to this part of the area connecting first negative clones title+"_"+i, // reduce the PSF cell size to this part of the area connecting first negative clones
(globalDebugLevel>4), (globalDebugLevel>4),
globalDebugLevel); globalDebugLevel);
if (globalDebugLevel>2) System.out.println(x0+":"+y0+"After-1: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts [i][0],3)+" PSF_shifts["+i+"][1]="+IJ.d2s( PSF_shifts[i][1],3)); if (globalDebugLevel>debugThreshold) System.out.println(x0+":"+y0+"After-1: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts [i][0],3)+" PSF_shifts["+i+"][1]="+IJ.d2s( PSF_shifts[i][1],3));
if (globalDebugLevel>2) System.out.println(x0+":"+y0+"After-1: color Component "+i+" PSF_centroids["+i+"][0]="+IJ.d2s(PSF_centroids[i][0],3)+" PSF_centroids["+i+"][1]="+IJ.d2s(PSF_centroids[i][1],3)); if (globalDebugLevel>debugThreshold) System.out.println(x0+":"+y0+"After-1: color Component "+i+" PSF_centroids["+i+"][0]="+IJ.d2s(PSF_centroids[i][0],3)+" PSF_centroids["+i+"][1]="+IJ.d2s(PSF_centroids[i][1],3));
lateralChromatic[i]=shiftBayerToSensor ( PSF_shifts[i][0]+PSF_centroids[i][0], lateralChromatic[i]=shiftBayerToSensor ( PSF_shifts[i][0]+PSF_centroids[i][0],
PSF_shifts[i][1]+PSF_centroids[i][1], PSF_shifts[i][1]+PSF_centroids[i][1],
i, i,
...@@ -2873,9 +2875,10 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -2873,9 +2875,10 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
} }
if (globalDebugLevel>1) { //1 if (globalDebugLevel>1) { //1
for (i=0;i<PSF_shifts.length;i++) if (colorComponents.colorsToCorrect[i]){ for (i=0;i<PSF_shifts.length;i++) if (colorComponents.colorsToCorrect[i]){
if (globalDebugLevel>2) { //2 if (globalDebugLevel>debugThreshold) { //2
System.out.println(x0+":"+y0+" Color Component "+i+" subpixel="+subpixel+ System.out.println(x0+":"+y0+" Color Component "+i+" subpixel="+subpixel+
" psfParameters.ignoreChromatic="+psfParameters.ignoreChromatic+ " psfParameters.ignoreChromatic="+psfParameters.ignoreChromatic+
" psfParameters.absoluteCenter="+psfParameters.absoluteCenter+
" psfParameters.symm180="+psfParameters.symm180); " psfParameters.symm180="+psfParameters.symm180);
System.out.println(x0+":"+y0+ " PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+ System.out.println(x0+":"+y0+ " PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+
" PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3)+ " PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3)+
...@@ -3339,7 +3342,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -3339,7 +3342,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
debugLevel); debugLevel);
// true); // true);
if (!master && !psfParameters.ignoreChromatic && psfParameters.centerPSF && (centerXY!=null)){ if (!master && !psfParameters.ignoreChromatic && !psfParameters.absoluteCenter && psfParameters.centerPSF && (centerXY!=null)){
// System.out.println("1:pixelsPSF.length="+pixelsPSF.length+" outSize+"+outSize); // System.out.println("1:pixelsPSF.length="+pixelsPSF.length+" outSize+"+outSize);
// TODO: Shift +/- 0.5 Pix here {centerXY[0]-Math.round(centerXY[0]),centerXY[1]-Math.round(centerXY[1])} // TODO: Shift +/- 0.5 Pix here {centerXY[0]-Math.round(centerXY[0]),centerXY[1]-Math.round(centerXY[1])}
...@@ -3397,7 +3400,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -3397,7 +3400,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
if (debugLevel>2) System.out.println("Centroid after first binPSF: x="+IJ.d2s(centroidXY[0],3)+" y="+IJ.d2s(centroidXY[1],3)+" center was at x="+IJ.d2s(centerXY[0],3)+" y="+IJ.d2s(centerXY[1],3)); if (debugLevel>2) System.out.println("Centroid after first binPSF: x="+IJ.d2s(centroidXY[0],3)+" y="+IJ.d2s(centroidXY[1],3)+" center was at x="+IJ.d2s(centerXY[0],3)+" y="+IJ.d2s(centerXY[1],3));
/* Re-bin results with the new center if ignoreChromatic is true, update centerXY[](shift of the result PSF array) and centroidXY[] (center of the optionally shifted PDF array) */ /* Re-bin results with the new center if ignoreChromatic is true, update centerXY[](shift of the result PSF array) and centroidXY[] (center of the optionally shifted PDF array) */
if (master || psfParameters.ignoreChromatic) { if (!psfParameters.absoluteCenter && (master || psfParameters.ignoreChromatic)) {
if (centerXY!=null) { if (centerXY!=null) {
centerXY[0]+=centroidXY[0]; centerXY[0]+=centroidXY[0];
centerXY[1]+=centroidXY[1]; centerXY[1]+=centroidXY[1];
...@@ -4908,6 +4911,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -4908,6 +4911,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
public boolean useWindow; public boolean useWindow;
public boolean symm180; public boolean symm180;
public boolean ignoreChromatic; public boolean ignoreChromatic;
public boolean absoluteCenter;
public double smoothSeparate; public double smoothSeparate;
public double topCenter; public double topCenter;
public double sigmaToRadius; public double sigmaToRadius;
...@@ -4927,6 +4931,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -4927,6 +4931,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
boolean useWindow, boolean useWindow,
boolean symm180, boolean symm180,
boolean ignoreChromatic, boolean ignoreChromatic,
boolean absoluteCenter,
double smoothSeparate, double smoothSeparate,
double topCenter, double topCenter,
double sigmaToRadius, double sigmaToRadius,
...@@ -4946,6 +4951,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -4946,6 +4951,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
this.useWindow = useWindow; this.useWindow = useWindow;
this.symm180 = symm180; this.symm180 = symm180;
this.ignoreChromatic = ignoreChromatic; this.ignoreChromatic = ignoreChromatic;
this.absoluteCenter=absoluteCenter;
this.smoothSeparate = smoothSeparate; this.smoothSeparate = smoothSeparate;
this.topCenter = topCenter; this.topCenter = topCenter;
this.sigmaToRadius = sigmaToRadius; this.sigmaToRadius = sigmaToRadius;
...@@ -4968,6 +4974,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -4968,6 +4974,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
this.useWindow, this.useWindow,
this.symm180, this.symm180,
this.ignoreChromatic, this.ignoreChromatic,
this.absoluteCenter,
this.smoothSeparate, this.smoothSeparate,
this.topCenter, this.topCenter,
this.sigmaToRadius, this.sigmaToRadius,
...@@ -4988,6 +4995,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -4988,6 +4995,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
properties.setProperty(prefix+"useWindow",this.useWindow+""); properties.setProperty(prefix+"useWindow",this.useWindow+"");
properties.setProperty(prefix+"symm180",this.symm180+""); properties.setProperty(prefix+"symm180",this.symm180+"");
properties.setProperty(prefix+"ignoreChromatic",this.ignoreChromatic+""); properties.setProperty(prefix+"ignoreChromatic",this.ignoreChromatic+"");
properties.setProperty(prefix+"absoluteCenter",this.absoluteCenter+"");
properties.setProperty(prefix+"smoothSeparate",this.smoothSeparate+""); properties.setProperty(prefix+"smoothSeparate",this.smoothSeparate+"");
properties.setProperty(prefix+"topCenter",this.topCenter+""); properties.setProperty(prefix+"topCenter",this.topCenter+"");
properties.setProperty(prefix+"sigmaToRadius",this.sigmaToRadius+""); properties.setProperty(prefix+"sigmaToRadius",this.sigmaToRadius+"");
...@@ -5007,6 +5015,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -5007,6 +5015,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
properties.setProperty(prefix+"useWindow",this.useWindow+""); properties.setProperty(prefix+"useWindow",this.useWindow+"");
properties.setProperty(prefix+"symm180",this.symm180+""); properties.setProperty(prefix+"symm180",this.symm180+"");
properties.setProperty(prefix+"ignoreChromatic",this.ignoreChromatic+""); properties.setProperty(prefix+"ignoreChromatic",this.ignoreChromatic+"");
properties.setProperty(prefix+"absoluteCenter",this.absoluteCenter+"");
properties.setProperty(prefix+"smoothSeparate",this.smoothSeparate+""); properties.setProperty(prefix+"smoothSeparate",this.smoothSeparate+"");
properties.setProperty(prefix+"topCenter",this.topCenter+""); properties.setProperty(prefix+"topCenter",this.topCenter+"");
properties.setProperty(prefix+"sigmaToRadius",this.sigmaToRadius+""); properties.setProperty(prefix+"sigmaToRadius",this.sigmaToRadius+"");
...@@ -5027,6 +5036,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -5027,6 +5036,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
if (properties.getProperty(prefix+"useWindow")!=null) this.useWindow=Boolean.parseBoolean(properties.getProperty(prefix+"useWindow")); if (properties.getProperty(prefix+"useWindow")!=null) this.useWindow=Boolean.parseBoolean(properties.getProperty(prefix+"useWindow"));
if (properties.getProperty(prefix+"symm180")!=null) this.symm180=Boolean.parseBoolean(properties.getProperty(prefix+"symm180")); if (properties.getProperty(prefix+"symm180")!=null) this.symm180=Boolean.parseBoolean(properties.getProperty(prefix+"symm180"));
if (properties.getProperty(prefix+"ignoreChromatic")!=null) this.ignoreChromatic=Boolean.parseBoolean(properties.getProperty(prefix+"ignoreChromatic")); if (properties.getProperty(prefix+"ignoreChromatic")!=null) this.ignoreChromatic=Boolean.parseBoolean(properties.getProperty(prefix+"ignoreChromatic"));
if (properties.getProperty(prefix+"absoluteCenter")!=null) this.absoluteCenter=Boolean.parseBoolean(properties.getProperty(prefix+"absoluteCenter"));
if (properties.getProperty(prefix+"smoothSeparate")!=null) this.smoothSeparate=Double.parseDouble(properties.getProperty(prefix+"smoothSeparate")); if (properties.getProperty(prefix+"smoothSeparate")!=null) this.smoothSeparate=Double.parseDouble(properties.getProperty(prefix+"smoothSeparate"));
if (properties.getProperty(prefix+"topCenter")!=null) this.topCenter=Double.parseDouble(properties.getProperty(prefix+"topCenter")); if (properties.getProperty(prefix+"topCenter")!=null) this.topCenter=Double.parseDouble(properties.getProperty(prefix+"topCenter"));
if (properties.getProperty(prefix+"sigmaToRadius")!=null) this.sigmaToRadius=Double.parseDouble(properties.getProperty(prefix+"sigmaToRadius")); if (properties.getProperty(prefix+"sigmaToRadius")!=null) this.sigmaToRadius=Double.parseDouble(properties.getProperty(prefix+"sigmaToRadius"));
......
src/main/java/MatchSimulatedPattern.java
View file @ 7d08fe37
...@@ -3350,8 +3350,10 @@ public class MatchSimulatedPattern { ...@@ -3350,8 +3350,10 @@ public class MatchSimulatedPattern {
if (!updating){ if (!updating){
double [][] node=gn.getNode(); double [][] node=gn.getNode();
double [] centerXY=node[0]; double [] centerXY=node[0];
if (global_debug_level>1) { if (global_debug_level>0) {
System.out.println("distortions: node X/Y are "+centerXY[0]+"/"+centerXY[1]); // System.out.println("distortions: node X/Y are "+centerXY[0]+"/"+centerXY[1]);
System.out.println("distortions: nodeQueue has "+(debug_left--)+" candidates left (including this one) :node X/Y are "+centerXY[0]+"/"+centerXY[1]);
} }
// if (debugLevel>1) { // if (debugLevel>1) {
if (global_debug_level>1) { if (global_debug_level>1) {
...@@ -3374,7 +3376,6 @@ public class MatchSimulatedPattern { ...@@ -3374,7 +3376,6 @@ public class MatchSimulatedPattern {
if (global_debug_level>1) { if (global_debug_level>1) {
System.out.println("putInWaveList(waveFrontList, {"+centerUV[0]+","+centerUV[1]+"}, 0);"); System.out.println("putInWaveList(waveFrontList, {"+centerUV[0]+","+centerUV[1]+"}, 0);");
} }
} }
// Each layer processing may be multi-threaded, they join before going to the next layer // Each layer processing may be multi-threaded, they join before going to the next layer
...@@ -3453,7 +3454,7 @@ public class MatchSimulatedPattern { ...@@ -3453,7 +3454,7 @@ public class MatchSimulatedPattern {
layer++; layer++;
if (updateStatus) IJ.showStatus("Correlating patterns, layer "+layer+(cleanup.get()?"(cleanup)":"")+", length "+waveFrontList.size()); if (updateStatus) IJ.showStatus("Correlating patterns, layer "+layer+(cleanup.get()?"(cleanup)":"")+", length "+waveFrontList.size());
// if (debugLevel>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size()); // if (debugLevel>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size());
if (global_debug_level>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size()); if (global_debug_level>2) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size());
// starting layer // starting layer
cellNum.set(0); cellNum.set(0);
for (int ithread = 0; ithread < threads.length; ithread++) { for (int ithread = 0; ithread < threads.length; ithread++) {
...@@ -4077,11 +4078,10 @@ public class MatchSimulatedPattern { ...@@ -4077,11 +4078,10 @@ public class MatchSimulatedPattern {
); );
if ((node!=null) && (node[0]!=null)) { if ((node!=null) && (node[0]!=null)) {
nodeQueue.add(new GridNode(node)); nodeQueue.add(new GridNode(node));
if (debugLevel>1) System.out.println("probing "+n); if (debugLevel>1) System.out.println("adding candidate "+n+" x0="+point[0]+" y0="+point[1]+" -> "+ node[0][0]+"/"+node[0][1]);
} }
} }
triedIndices[n]=true; // regardless - good or bad triedIndices[n]=true; // regardless - good or bad
} }
} }
}; };
......
src/main/java/aberrations.java
View file @ 7d08fe37
...@@ -141,6 +141,8 @@ Panel panel1,panel2; ...@@ -141,6 +141,8 @@ Panel panel1,panel2;
public static double OTF_deconvInvert = 0.007; // 0.015; // 0.01; // when FFT component is less than this fraction of the maximal value, replace 1/z with Z public static double OTF_deconvInvert = 0.007; // 0.015; // 0.01; // when FFT component is less than this fraction of the maximal value, replace 1/z with Z
/* TODO: check why combined greens result in center at x=-0.532/2 , y= -.0272/2 */ /* TODO: check why combined greens result in center at x=-0.532/2 , y= -.0272/2 */
public static boolean PSF_ignoreChromatic= false; // ignore lateral chromatic aberration (center OTF to 0,0) public static boolean PSF_ignoreChromatic= false; // ignore lateral chromatic aberration (center OTF to 0,0)
public static boolean OTF_fold = false; // fold high frequency to lower when downsampling pixels (before inverse FFT) public static boolean OTF_fold = false; // fold high frequency to lower when downsampling pixels (before inverse FFT)
public static double PSF_cutoff_energy=0.9; // Limit result kernel to proportional of the PSF, calculate initial cluster shape by this cutoff energy public static double PSF_cutoff_energy=0.9; // Limit result kernel to proportional of the PSF, calculate initial cluster shape by this cutoff energy
......
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