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Commit 10143f8f authored by Andrey Filippov's avatar Andrey Filippov
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committing w/o breaking - 6

parent 069dd00f
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src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java
View file @ 10143f8f
......@@ -9163,9 +9163,10 @@ if (MORE_BUTTONS) {
EYESIS_ABERRATIONS.createPartialKernels(
this.SYNC_COMMAND.stopRequested,
MAP_FFT_SIZE, // scanImageForPatterns:FFT size //int mapFFTsize, // scanImageForPatterns:FFT size
FFT_OVERLAP, ////int fft_overlap,
FFT_SIZE, //int fft_size,
LWIR_PARAMETERS,
// MAP_FFT_SIZE, // scanImageForPatterns:FFT size //int mapFFTsize, // scanImageForPatterns:FFT size
// FFT_OVERLAP, ////int fft_overlap,
// FFT_SIZE, //int fft_size,
PSF_SUBPIXEL, // //int PSF_subpixel,
OTF_FILTER, // //OTFFilterParameters otfFilterParameters,
PSF_PARS, //PSFParameters psfParameters,
src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java
View file @ 10143f8f
......@@ -14,6 +14,7 @@ import com.elphel.imagej.common.DoubleGaussianBlur;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.common.WindowTools;
import com.elphel.imagej.jp4.JP46_Reader_camera;
import com.elphel.imagej.lwir.LwirReaderParameters;
import ij.IJ;
import ij.ImagePlus;
......@@ -1056,15 +1057,12 @@ public class EyesisAberrations {
}
return fileList;
}
/*
int numChannels=this.fittingStrategy.distortionCalibrationData.getNumChannels(); // number of used channels
*/
public boolean createPartialKernels(
public boolean createPartialKernels(
AtomicInteger stopRequested, // 1 - stop now, 2 - when convenient
int mapFFTsize, // scanImageForPatterns:FFT size
int fft_overlap,
int fft_size,
LwirReaderParameters lwirReaderParameters, // null is OK
// int fft_overlap,
// int fft_size,
int PSF_subpixel,
OTFFilterParameters otfFilterParameters,
PSFParameters psfParameters,
......@@ -1245,6 +1243,10 @@ public class EyesisAberrations {
if (debugLevel>0) System.out.println("Processing file #"+(imgNum+1)+ " ( of "+files.length+") :"+files[imgNum][0]);
ImagePlus imp=new ImagePlus(files[imgNum][0]); // read source file
JP4_INSTANCE.decodeProperiesFromInfo(imp);
boolean is_lwir = lwirReaderParameters.is_LWIR(imp);
int fft_size = is_lwir ? distortionParameters.FFTSize_lwir : distortionParameters.FFTSize;
int fft_overlap = is_lwir ? distortionParameters.FFTOverlap_lwir : distortionParameters.FFTOverlap;
imp.setProperty("MONOCHROME",""+is_lwir);
// pad image to full sensor size
int numGridImage=fileIndices[imgNum];
int chn = distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].getChannel();
......@@ -1335,7 +1337,7 @@ public class EyesisAberrations {
null, // int [][][] sampleList, // optional (or null) 2-d array: list of coordinate pairs (2d - to match existent PSF_KERNEL_MAP structure)
multiFilePSF.overexposedMaxFraction, //MULTIFILE_PSF.overexposedMaxFraction,
simulParameters, //SIMUL, //simulation parameters
mapFFTsize, // MAP_FFT_SIZE, // scanImageForPatterns:FFT size int mapFFTsize, // scanImageForPatterns:FFT size
// mapFFTsize, // MAP_FFT_SIZE, // scanImageForPatterns:FFT size int mapFFTsize, // scanImageForPatterns:FFT size
patternDetectParameters, //PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
fft_overlap, //FFT_OVERLAP, // int fft_overlap,
fft_size, // FFT_SIZE, // int fft_size,
......@@ -2237,11 +2239,11 @@ public class EyesisAberrations {
public double [][][][] createPSFMap(
final MatchSimulatedPattern commonMatchSimulatedPattern, // to be cloned in threads, using common data
final ImagePlus imp_sel, // linearized Bayer mosaic image from the camera, GR/BG
final ImagePlus imp_sel, // linearized Bayer mosaic image from the camera, GR/BG
final int [][][] sampleList, // optional (or null) 2-d array: list of coordinate pairs (2d - to match existent pdfKernelMap structure)
final double overexposedAllowed, // fraction of pixels OK to be overexposed
final SimulationPattern.SimulParameters simulParameters,
final int mapFFTsize, // scanImageForPatterns:FFT size
// final int mapFFTsize, // scanImageForPatterns:FFT size
final MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
final int fft_overlap,
final int fft_size,
......@@ -2279,7 +2281,7 @@ public class EyesisAberrations {
imp_sel.getWidth(), // image (mask) width
fft_size*2,
fft_overlap*2,
fft_size, // backward compatibility margin==tileSize/2
fft_size, // backward compatibility margin==tileSize/2
gaussWidth,
// psfParameters.minDefinedArea);
minDefinedArea,
......@@ -2309,7 +2311,7 @@ public class EyesisAberrations {
tilesToProcessXY[ncell ][1]=nTileY;
tilesToProcessXY[ncell ][2]=(sampleList==null)?(fft_overlap*2*nTileX):sampleList[nTileY][nTileX][0];
tilesToProcessXY[ncell++][3]=(sampleList==null)?(fft_overlap*2*nTileY):sampleList[nTileY][nTileX][1];
pdfKernelMap[nTileY][nTileX]=new double[colorComponents.colorsToCorrect.length][];
pdfKernelMap[nTileY][nTileX]=new double[colorComponents.colorsToCorrect.length][];
} else pdfKernelMap[nTileY][nTileX]=null;
}
final double [][][][] debugLateral=new double [PSFBooleanMap.length][PSFBooleanMap[0].length][][];
......@@ -2652,39 +2654,39 @@ public class EyesisAberrations {
public double [][] getPSFKernels ( ImagePlus imp,
float [][] simArray, //simulation image, scaled PSF_subpixel/2 (or null), [0] - main pixels, [1] - shifted diagonally by 0.5 pixels (for checker greens)
int size, // size in pixels (twice FFT_SIZE)
int x0, // top left corner X (pixels)
int y0, // top left corner Y (pixels)
float [][] simArray, //simulation image, scaled PSF_subpixel/2 (or null), [0] - main pixels, [1] - shifted diagonally by 0.5 pixels (for checker greens)
int tile_size, // size in pixels (twice FFT_SIZE)
int x0, // top left corner X (pixels)
int y0, // top left corner Y (pixels)
SimulationPattern simulationPattern,
MatchSimulatedPattern matchSimulatedPattern,
MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
double [] Hamming, //=initHamming( fft_size) calculate once
double [] fullHamming, //=initHamming( fft_size*subpixel);
int subpixel, // use finer grid than actual pixels
double [] Hamming, //=initHamming( fft_size) calculate once
double [] fullHamming, //=initHamming( fft_size*subpixel);
int subpixel, // use finer grid than actual pixels
SimulationPattern.SimulParameters simulParameters,
EyesisAberrations.ColorComponents colorComponents,
EyesisAberrations.OTFFilterParameters otfFilterParameters,
int referenceComp, // number of color component to reference lateral chromatic aberration to (now 4 - checkerboard greens)
int referenceComp, // number of color component to reference lateral chromatic aberration to (now 4 - checkerboard greens)
EyesisAberrations.PSFParameters psfParameters,
DoubleFHT fht_instance, // provide DoubleFHT instance to save on initializations (or null)
int masterDebugLevel, // get rid of it? // ** NEW
int globalDebugLevel,// ** NEW
int debug,
double [][] debugLateralTile
int masterDebugLevel, // get rid of it? // ** NEW
int globalDebugLevel,// ** NEW
int debug,
double [][] debugLateralTile
){
boolean debugThis=false; //(y0==384) && ((x0==448) || (x0==512));
if (globalDebugLevel>1){
System.out.println("getPSFKernels(), simArray is "+((simArray==null)?"":"not ")+"null");
}
boolean is_mono = false;
if (imp==null) return null; // Maybe convert to double pixel array once to make it faster?
if (fht_instance==null) fht_instance=new DoubleFHT(); // move upstream to reduce number of initializations
double [][] kernels= new double[6][]; // was global
String title=imp.getTitle()+"X"+x0+"Y"+y0;
Rectangle PSFCell=new Rectangle (x0,y0,size,size);
int fft_size=size/2;
double [][] input_bayer=matchSimulatedPattern.splitBayer(imp,PSFCell,colorComponents.equalizeGreens); // does it work trhe same?
Rectangle PSFCell=new Rectangle (x0,y0,tile_size,tile_size);
int fft_size=tile_size/2;
double [][] input_bayer_or_mono=matchSimulatedPattern.splitBayer(imp,PSFCell,colorComponents.equalizeGreens); // does it work trhe same?
//int greensToProcess=4;
int i,j,l;
double [][] simul_pixels;
......@@ -2698,7 +2700,7 @@ public class EyesisAberrations {
if ((simArray==null) || (psfParameters.approximateGrid)){ // just for testing(never here?)
/* Calculate pattern parameters, including distortion */
if (matchSimulatedPattern.PATTERN_GRID==null) {
double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(input_bayer, // pixel array to process (no windowing!)
double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(input_bayer_or_mono, // pixel array to process (no windowing!)
patternDetectParameters,
patternDetectParameters.minGridPeriod/2,
patternDetectParameters.maxGridPeriod/2,
......@@ -2737,7 +2739,7 @@ public class EyesisAberrations {
double[][] distPatPars= matchSimulatedPattern.findPatternFromGrid(
x0, // top-left pixel of the square WOI
y0,
size, // size of square (pixels)
tile_size, // size of square (pixels)
Hamming, // only half-window!
false, // use linear approximation (instead of quadratic)
1.0E-10, // thershold ratio of matrix determinant to norm for linear approximation (det too low - fail)
......@@ -2755,12 +2757,10 @@ public class EyesisAberrations {
double [] phases={
1.0*Math.PI*(distPatPars[0][2]-iUV[0]+(negative?(-0.5):0.5)), // measured from the center of white
1.0*Math.PI*(distPatPars[1][2]-iUV[1]+0.5)};
// double [][]wVectors={{distPatPars[0][0],distPatPars[0][1]},{distPatPars[1][0],distPatPars[1][1]}};
wVectors[0][0]=distPatPars[0][0];
wVectors[0][1]=distPatPars[0][1];
wVectors[1][0]=distPatPars[1][0];
wVectors[1][1]=distPatPars[1][1];
// simulationPattern.simulatePatternFullPattern( // Not thread safe!
localBarray=simulationPattern.simulatePatternFullPatternSafe(
wVectors[0][0],
wVectors[0][1],
......@@ -2774,14 +2774,13 @@ public class EyesisAberrations {
simulParameters.center_for_g2,
false);//boolean mono
}
// simul_pixels= simulationPattern.extractSimulPatterns (
simul_pixels= simulationPattern.extractSimulPatterns (
localBarray, // this version is thread safe
simulParameters,
subpixel, // subdivide pixels
fft_size*subpixel, // number of Bayer cells in width of the square selection (half number of pixels)
0.0, // selection center, X (in pixels)
0.0); // selection center, y (in pixels)
simul_pixels= simulationPattern.extractSimulPatterns (
localBarray, // this version is thread safe
simulParameters,
subpixel, // subdivide pixels
fft_size*subpixel, // number of Bayer cells in width of the square selection (half number of pixels)
0.0, // selection center, X (in pixels)
0.0); // selection center, y (in pixels)
if (subpixel>1) {
if (colorComponents.colorsToCorrect[5]) simul_pixels=combineCheckerGreens (simul_pixels, // pixel arrays after oversampleFFTInput() or extractSimulPatterns())
subpixel); // same as used in oversampleFFTInput() - oversampling ratio
......@@ -2791,23 +2790,20 @@ public class EyesisAberrations {
}
simul_pixels= normalizeAndWindow (simul_pixels, fullHamming);
} else {
Rectangle PSFCellSim=new Rectangle (x0*subpixel/2,y0*subpixel/2,size*subpixel/2,size*subpixel/2); // getting here
simul_pixels=new double[6][];
// simulationPattern.debugLevel=globalDebugLevel;
for (i=0;i<simul_pixels.length; i++) {
if (colorComponents.colorsToCorrect[i]) simul_pixels[i]=simulationPattern.extractBayerSim (
simArray, // [0] - regular pixels, [1] - shifted by 1/2 diagonally, for checker greens
imgWidth*subpixel/2,
PSFCellSim,
subpixel, // 4
i);
else simul_pixels[i]=null;
}
//System.out.println("PSFCell.y="+PSFCell.y+" PSFCell.height="+PSFCell.height+" imgWidth="+imgWidth+" PSFCell.x="+PSFCell.x+" PSFCell.width="+PSFCell.width+" matchSimulatedPattern.UV_INDEX.length="+matchSimulatedPattern.UV_INDEX.length);
} else {
Rectangle PSFCellSim=new Rectangle (x0*subpixel/2,y0*subpixel/2,tile_size*subpixel/2,tile_size*subpixel/2); // getting here
simul_pixels=new double[6][];
for (i=0;i<simul_pixels.length; i++) {
if (colorComponents.colorsToCorrect[i]) simul_pixels[i]=simulationPattern.extractBayerSim (
simArray, // [0] - regular pixels, [1] - shifted by 1/2 diagonally, for checker greens
imgWidth*subpixel/2,
PSFCellSim,
subpixel, // 4
i);
else simul_pixels[i]=null;
}
int index=matchSimulatedPattern.getUVIndex((PSFCell.y+PSFCell.height/2)*imgWidth+(PSFCell.x+PSFCell.width/2));
// int index=matchSimulatedPattern.getUVIndex((PSFCell.y+PSFCell.height/2)*matchSimulatedPattern.getWOI().width+(PSFCell.x+PSFCell.width/2));
if (index<0) {
System.out.println ("Error, No UV pattern @ x="+(PSFCell.x+PSFCell.width/2)+", y="+(PSFCell.y+PSFCell.height/2));
......@@ -2833,7 +2829,7 @@ public class EyesisAberrations {
wVectors[1]=matchSimulatedPattern.getDArray(iUV[1],iUV[0],2);
// should it be averaged WV?
if (globalDebugLevel>2) System.out.println ( " x0="+x0+" y0="+y0);
if (globalDebugLevel>2) SDFA_INSTANCE.showArrays(input_bayer, true, title+"-in");
if (globalDebugLevel>2) SDFA_INSTANCE.showArrays(input_bayer_or_mono, true, title+"-in");
if (globalDebugLevel>2) SDFA_INSTANCE.showArrays(simul_pixels, true, title+"-S");
//if (globalDebugLevel>2) System.out.println (simArray[0][-1]); // cause error
if (masterDebugLevel>1){
......@@ -2846,21 +2842,21 @@ public class EyesisAberrations {
simul_pixels= normalizeAndWindow (simul_pixels, fullHamming);
}
input_bayer= normalizeAndWindow (input_bayer, Hamming);
input_bayer_or_mono= normalizeAndWindow (input_bayer_or_mono, Hamming);
if (subpixel>1) {
input_bayer= oversampleFFTInput (input_bayer,subpixel);
if (colorComponents.colorsToCorrect[5]) input_bayer=combineCheckerGreens (input_bayer, // pixel arrays after oversampleFFTInput() or extractSimulPatterns())
input_bayer_or_mono= oversampleFFTInput (input_bayer_or_mono,subpixel);
if (colorComponents.colorsToCorrect[5]) input_bayer_or_mono=combineCheckerGreens (input_bayer_or_mono, // pixel arrays after oversampleFFTInput() or extractSimulPatterns())
subpixel); // same as used in oversampleFFTInput() - oversampling ratio
}
for (i=0;i<4;i++) if (!colorComponents.colorsToCorrect[i]) input_bayer[i]=null; // leave composite greens even if disabled
for (i=0;i<4;i++) if (!colorComponents.colorsToCorrect[i]) input_bayer_or_mono[i]=null; // leave composite greens even if disabled
if (debugThis) {
// SDFA_INSTANCE.showArrays(input_bayer, fft_size*subpixel, fft_size*subpixel, title);
}
if (globalDebugLevel>2) System.out.println ( " input_bayer.length="+input_bayer.length+" simul_pixels.length="+simul_pixels.length+" fft_size*subpixel="+fft_size*subpixel);
for (i=0;(i<input_bayer.length) && (i<simul_pixels.length);i++) if ((colorComponents.colorsToCorrect[i]) && (input_bayer[i]!=null)){
if (globalDebugLevel>2) System.out.println ( "input_bayer["+i+"].length="+input_bayer[i].length+" simul_pixels["+i+"].length="+simul_pixels[i].length);
if (globalDebugLevel>2) System.out.println ( " input_bayer.length="+input_bayer_or_mono.length+" simul_pixels.length="+simul_pixels.length+" fft_size*subpixel="+fft_size*subpixel);
for (i=0;(i<input_bayer_or_mono.length) && (i<simul_pixels.length);i++) if ((colorComponents.colorsToCorrect[i]) && (input_bayer_or_mono[i]!=null)){
if (globalDebugLevel>2) System.out.println ( "input_bayer["+i+"].length="+input_bayer_or_mono[i].length+" simul_pixels["+i+"].length="+simul_pixels[i].length);
}
if (debugThis) SDFA_INSTANCE.showArrays(input_bayer, true, title+"-input");
if (debugThis) SDFA_INSTANCE.showArrays(input_bayer_or_mono, true, title+"-input");
if (debugThis) SDFA_INSTANCE.showArrays(simul_pixels, true, title+"-SIM");
//if (globalDebugLevel>2)globalDebugLevel=0; //************************************************************
......@@ -2868,44 +2864,45 @@ public class EyesisAberrations {
double wvAverage=Math.sqrt(0.5*(wVectors[0][0]*wVectors[0][0]+wVectors[0][1]*wVectors[0][1]+
wVectors[1][0]*wVectors[1][0]+wVectors[1][1]*wVectors[1][1]));
for (i=0;(i<input_bayer.length) && (i<simul_pixels.length);i++) if ((colorComponents.colorsToCorrect[i]) && (input_bayer[i]!=null)){
if (globalDebugLevel>2) System.out.println ( "Color "+colorComponents.getColorName(i)+" is re-calculated into bayer pixels ");
if (globalDebugLevel>2) System.out.println ( "input_bayer["+i+"].length="+input_bayer[i].length+" simul_pixels["+i+"].length="+simul_pixels[i].length);
inverted[i]=limitedInverseOfFHT(input_bayer[i],
simul_pixels[i],
fft_size*subpixel,
(i==5), // boolean checker // checkerboard pattern in the source file (use when filtering)
true, // forwardOTF,
subpixel,
otfFilterParameters,
fht_instance,
psfParameters.mask1_sigma*size*wvAverage, // normalize to wave vectors!
psfParameters.mask1_threshold,
psfParameters.gaps_sigma*size*wvAverage,
psfParameters.mask_denoise,
debug,
globalDebugLevel,
title+"-"+i);
}
for (i=0;(i<input_bayer_or_mono.length) && (i<simul_pixels.length);i++) if ((colorComponents.colorsToCorrect[i]) && (input_bayer_or_mono[i]!=null)){
if (globalDebugLevel>2) System.out.println ( "Color "+colorComponents.getColorName(i)+" is re-calculated into bayer pixels ");
if (globalDebugLevel>2) System.out.println ( "input_bayer["+i+"].length="+input_bayer_or_mono[i].length+" simul_pixels["+i+"].length="+simul_pixels[i].length);
inverted[i]=limitedInverseOfFHT(input_bayer_or_mono[i],
simul_pixels[i],
fft_size*subpixel,
(i==5), // boolean checker // checkerboard pattern in the source file (use when filtering)
true, // forwardOTF,
subpixel,
otfFilterParameters,
fht_instance,
psfParameters.mask1_sigma*tile_size*wvAverage, // normalize to wave vectors!
psfParameters.mask1_threshold,
psfParameters.gaps_sigma*tile_size*wvAverage,
psfParameters.mask_denoise,
debug,
globalDebugLevel,
title+"-"+i);
}
int debugThreshold=1;
if (debugThis) SDFA_INSTANCE.showArrays(inverted, fft_size*subpixel, fft_size*subpixel, title+"_Combined-PSF");
/* correct composite greens */
/* Here we divide wave vectors by subpixel as the pixels are already added */
double [][] wVrotMatrix= {{0.5,0.5},{-0.5,0.5}};
double [][]wVectors4= new double [2][2];
double [][]wVectors4= new double [2][2]; // Will only be used for color, combined diagonal greens
for (i=0;i<2;i++) for (j=0;j<2;j++) {
wVectors4[i][j]=0.0;
for (l=0;l<2;l++) wVectors4[i][j]+=wVectors[i][l]*wVrotMatrix[l][j];
}
double [][] PSF_shifts= new double [input_bayer.length][]; // X/Y shift of the PSF array, in Bayer component pixel coordinates (same as PSF arrays)
double [][] PSF_centroids= new double [input_bayer.length][]; // X/Y coordinates of the centroids of PSF in Bayer component pioxel coordinates (same as PSF arrays) (after they were optionally shifted)
double [][] lateralChromatic= new double [input_bayer.length][]; // X/Y coordinates of the centroids of Bayer component PSF in sensor pixel coordinates
double [][] kernelsForFFT= new double [input_bayer.length][];
double [][] psf_inverted= new double [input_bayer.length][];
double [][] psf_inverted_masked=new double [input_bayer.length][];
double [] lateralChromaticAbs=new double [input_bayer.length];
double [][] PSF_shifts = new double [input_bayer_or_mono.length][]; // X/Y shift of the PSF array, in Bayer component pixel coordinates (same as PSF arrays)
double [][] PSF_centroids = new double [input_bayer_or_mono.length][]; // X/Y coordinates of the centroids of PSF in Bayer component pioxel coordinates (same as PSF arrays) (after they were optionally shifted)
double [][] lateralChromatic = new double [input_bayer_or_mono.length][]; // X/Y coordinates of the centroids of Bayer component PSF in sensor pixel coordinates
double [][] kernelsForFFT = new double [input_bayer_or_mono.length][];
double [][] psf_inverted = new double [input_bayer_or_mono.length][];
double [][] psf_inverted_masked = new double [input_bayer_or_mono.length][];
double [] lateralChromaticAbs = new double [input_bayer_or_mono.length];
double [] zeroVector={0.0,0.0};
for (i=input_bayer.length-1;i>=0;i--) {
for (i=input_bayer_or_mono.length-1;i>=0;i--) {
if (colorComponents.colorsToCorrect[i]) {
PSF_shifts[i]= zeroVector.clone();
PSF_centroids[i]= zeroVector.clone();
......@@ -2922,15 +2919,15 @@ public class EyesisAberrations {
}
//int [][] clusterMask;
/* Start with referenceComp */
i= referenceComp;
if (globalDebugLevel>debugThreshold) {
System.out.println(x0+":"+y0+"1-PSF_shifts.length= "+PSF_shifts.length+" i="+i+" input_bayer.length="+input_bayer.length);
i = referenceComp; // now 0 for mono
if (globalDebugLevel > debugThreshold) {
System.out.println(x0+":"+y0+"1-PSF_shifts.length= "+PSF_shifts.length+" i="+i+" input_bayer.length="+input_bayer_or_mono.length);
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));
}
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)
!psfParameters.absoluteCenter, //true, // master, force ignoreChromatic
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
......@@ -2940,12 +2937,13 @@ public class EyesisAberrations {
title+"_"+i, // reduce the PSF cell size to this part of the area connecting first negative clones
(globalDebugLevel>4),
globalDebugLevel
);
);
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>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 && !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_or_mono.length;j++) if ((colorComponents.colorsToCorrect[j]) && (j!=referenceComp)) {
PSF_shifts[j]=shiftSensorToBayer (shiftBayerToSensor(PSF_shifts[referenceComp],referenceComp,subpixel),j,subpixel);
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));
}
......@@ -2956,10 +2954,12 @@ public class EyesisAberrations {
i,
subpixel);
lateralChromaticAbs[i]=Math.sqrt(lateralChromatic[i][0]*lateralChromatic[i][0]+lateralChromatic[i][1]*lateralChromatic[i][1]);
/* 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_or_mono.length;i++) if ((i!=referenceComp) && (colorComponents.colorsToCorrect[i])) {
// Will never get here for mono
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_or_mono.length);
System.out.println(x0+":"+y0+"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));
......@@ -2998,27 +2998,31 @@ public class EyesisAberrations {
" lateralChromatic["+i+"][1]="+IJ.d2s(lateralChromatic[i][1],3));
}
}
if (colorComponents.colorsToCorrect[referenceComp]) for (i=0;i<colorComponents.colorsToCorrect.length;i++) if ((colorComponents.colorsToCorrect[i])&& (i!=referenceComp)){
System.out.println("#!# "+x0+":"+y0+" "+colorComponents.getColorName(i)+" lateral chromatic (from green) "+IJ.d2s(lateralChromaticAbs[i],3)+"pix(sensor): ["+i+"][0]="+IJ.d2s(lateralChromatic[i][0]-lateralChromatic[referenceComp][0],3)+
" ["+i+"][1]="+IJ.d2s(lateralChromatic[i][1]-lateralChromatic[referenceComp][1],3));
if (colorComponents.colorsToCorrect[referenceComp]) {
for (i=0;i<colorComponents.colorsToCorrect.length;i++) {
if ((colorComponents.colorsToCorrect[i])&& (i!=referenceComp)){
System.out.println("#!# "+x0+":"+y0+" "+colorComponents.getColorName(i)+" lateral chromatic (from green) "+IJ.d2s(lateralChromaticAbs[i],3)+"pix(sensor): ["+i+"][0]="+IJ.d2s(lateralChromatic[i][0]-lateralChromatic[referenceComp][0],3)+
" ["+i+"][1]="+IJ.d2s(lateralChromatic[i][1]-lateralChromatic[referenceComp][1],3));
}
}
}
System.out.println("#!# "+x0+":"+y0+" "+"Lateral shift green from simulation "+IJ.d2s(lateralChromaticAbs[referenceComp],3)+"pix(sensor): ["+referenceComp+"][0]="+IJ.d2s(lateralChromatic[referenceComp][0],3)+
" ["+referenceComp+"][1]="+IJ.d2s(lateralChromatic[referenceComp][1],3));
}
if (debugLateralTile!=null) for (i=0;i<PSF_shifts.length;i++) {
if (colorComponents.colorsToCorrect[i]){
debugLateralTile[i]=new double [6];
debugLateralTile[i][0]=lateralChromatic[i][0];
debugLateralTile[i][1]=lateralChromatic[i][1];
debugLateralTile[i][2]=PSF_shifts[i][0];
debugLateralTile[i][3]=PSF_shifts[i][1];
debugLateralTile[i][4]=PSF_centroids[i][0];
debugLateralTile[i][5]=PSF_centroids[i][1];
} else {
debugLateralTile[i]=null;
if (debugLateralTile != null) {
for (i = 0; i < PSF_shifts.length; i++) {
if (is_mono || colorComponents.colorsToCorrect[i]){
debugLateralTile[i] = new double [6];
debugLateralTile[i][0] = lateralChromatic[i][0];
debugLateralTile[i][1] = lateralChromatic[i][1];
debugLateralTile[i][2] = PSF_shifts[i][0];
debugLateralTile[i][3] = PSF_shifts[i][1];
debugLateralTile[i][4] = PSF_centroids[i][0];
debugLateralTile[i][5] = PSF_centroids[i][1];
} else {
debugLateralTile[i] = null;
}
}
}
if (debugThis && (kernels!=null)){
int debugSize=0;
......
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