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imagej-elphel
Commit 9f0c8d98 authored by Andrey Filippov's avatar Andrey Filippov
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making grid calculation work for VNIR cameras and large cells

parent cba1fc01
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Showing with 516 additions and 338 deletions
src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java
View file @ 9f0c8d98
......@@ -375,11 +375,13 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
8.0, // 3.0, // correlationMaxOffset, // maximal distance between predicted and actual pattern node
3.0, // 2.0, // increase back to .5? was needed with fisheye. 5.0, // double correlationMinContrast, // minimal contrast for the pattern to pass
3.5, // 2.5, // correlationMinInitialContrast, // minimal contrast for the pattern of the center (initial point)
1.0, //this.correlationMinAbsoluteContrast, // minimal contrast for the pattern to pass, does not compensate for low ligt
// Absolute contrast is broken (05.29.2019), disabling it
0.0, // 1.0, //this.correlationMinAbsoluteContrast, // minimal contrast for the pattern to pass, does not compensate for low ligt
// TODO: adjust to a reasonable number
1.0, //this.correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point)
0.0, // 1.0, //this.correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point)
0.8, // scaleFirstPassContrast, // Decrease contrast of cells that are too close to the border to be processed in refinement pass
2.0, // public double contrastSelectSigmaCenter; // Gaussian sigma to select correlation centers (fraction of UV period), 0.02 (center spot)
0.1, // contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
0.5, //contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5
......@@ -9486,14 +9488,16 @@ if (MORE_BUTTONS) {
for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){
long startFileTime=System.nanoTime();
if (DEBUG_LEVEL>0){
System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing file # "+(this_file+1)+
" (of "+ sourceFilesList.length+"): " + numFiles);
System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing set "+(nset+1) +" (of "+
sourceFilesList.length+"), channel # "+(nfile + 1)+
" (of "+ sourceFilesList[nset].length+"), file " +(this_file + 1)+" (of "+ numFiles+ ") - "+sourceFilesList[nset][nfile]);
}
String grid_path = null;
if (saveGrids && !overwriteGrids){ // check if result already exists
i = sourceFilesList[nset][nfile].lastIndexOf('/');
if (i>0){
String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1);
String grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name;
grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name;
if ((new File(grid_path)).exists()){
if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")");
continue;
......@@ -9543,6 +9547,10 @@ if (MORE_BUTTONS) {
imp_sel, // image to process
THREADS_MAX);
ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints);
if (imp_calibrated == null) {
if (DEBUG_LEVEL> -1) System.out.println("Grid is empty !");
continue;
}
if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();
if (saveGrids){
FileSaver fs=new FileSaver(imp_calibrated);
......@@ -9550,10 +9558,11 @@ if (MORE_BUTTONS) {
if (srcDir==null){
saveGrids=false; // do not ask about the next ones too
} else {
String path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+imp_calibrated.getTitle();
if (UPDATE_STATUS) IJ.showStatus("Saving "+path);
if (DEBUG_LEVEL>0) System.out.println("-->>> Saving "+path+" - using "+numAbsolutePoints+" laser pointer references");
fs.saveAsTiffStack(path);
// String path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+imp_calibrated.getTitle();
// String path = gridDir + Prefs.getFileSeparator() + set_name+Prefs.getFileSeparator()+imp_calibrated.getTitle();
if (UPDATE_STATUS) IJ.showStatus("Saving "+grid_path);
if (DEBUG_LEVEL>0) System.out.println("-->>> Saving "+grid_path+" - using "+numAbsolutePoints+" laser pointer references");
fs.saveAsTiffStack(grid_path);
}
}
}
......@@ -9657,7 +9666,7 @@ if (MORE_BUTTONS) {
COMPONENTS.equalizeGreens,
imp_sel, // image to process
THREADS_MAX);
ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints);
ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints); //----
if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();
if (saveGrids){
FileSaver fs=new FileSaver(imp_calibrated);
......@@ -17224,8 +17233,10 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
pixels[4],
WVgreens, // wave vectors (same units as the pixels array)
// patternDetectParameters.corrRingWidth, // ring (around r=0.5 dist to opposite corr) width
0.1, // contrastSelectSigma
0.5, // contrastAverageSigma
2.0, // distortionParameters.contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
0.1, // distortionParameters.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
// 0.1, // contrastSelectSigma
// 0.5, // contrastAverageSigma
0.0, // x0, // center coordinates
0.0, //y0,
title)[0]; // title base for optional plots names
......@@ -20320,7 +20331,8 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
gd.addNumericField("Correlation minimal contrast for initial search (absolute)", distortionParameters.correlationMinAbsoluteInitialContrast, 3);
gd.addNumericField("Decrease contrast of cells that are too close to the border to be processed in refinement pass", distortionParameters.scaleFirstPassContrast, 3);
gd.addNumericField("Gaussian sigma to select correlation centers (fraction of UV period), 0.1", distortionParameters.contrastSelectSigma, 3);
gd.addNumericField("Gaussian sigma to select correlation center in pixels, 2.0", distortionParameters.contrastSelectSigmaCenter, 3);
gd.addNumericField("Gaussian sigma to select correlation off-centers (fraction of UV period), 0.1", distortionParameters.contrastSelectSigma, 3);
gd.addNumericField("Gaussian sigma to average correlation variations (as contrast reference), 0.5", distortionParameters.contrastAverageSigma, 3);
gd.addNumericField("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0);
......@@ -20401,13 +20413,14 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
distortionParameters.correlationMinAbsoluteContrast= gd.getNextNumber();
distortionParameters.correlationMinAbsoluteInitialContrast= gd.getNextNumber();
distortionParameters.scaleFirstPassContrast= gd.getNextNumber();
distortionParameters.contrastSelectSigma= gd.getNextNumber();
distortionParameters.contrastAverageSigma= gd.getNextNumber();
distortionParameters.scaleFirstPassContrast= gd.getNextNumber();
distortionParameters.contrastSelectSigmaCenter= gd.getNextNumber();
distortionParameters.contrastSelectSigma= gd.getNextNumber();
distortionParameters.contrastAverageSigma= gd.getNextNumber();
distortionParameters.minimalPatternCluster=(int) gd.getNextNumber();
distortionParameters.scaleMinimalInitialContrast=gd.getNextNumber();
distortionParameters.searchOverlap= gd.getNextNumber();
distortionParameters.searchOverlap= gd.getNextNumber();
distortionParameters.patternSubdiv= (int) gd.getNextNumber();
distortionParameters.bPatternSigma= gd.getNextNumber();
src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java
View file @ 9f0c8d98
......@@ -1111,11 +1111,10 @@ public class MatchSimulatedPattern {
/* ======================================================================== */
public double [] correlationContrast (
double [] pixels, // square pixel array
double [] widowedGreens, // array to normailze correlation result
double [] widowedGreens, // array to normalize correlation result
double [][] wVectors, // wave vectors (same units as the pixels array)
// double ringWidth, // ring (around r=0.5 dist to opposite corr) width
double contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
double contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5
double contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (in PIXELS), 2.0
double contrastSelectSigmaOther, // Gaussian sigma to select correlation off-centers centers (fraction of UV period), 0.1
double x0, // center coordinates
double y0,
......@@ -1124,25 +1123,12 @@ public class MatchSimulatedPattern {
return correlationContrast (
pixels, // square pixel array
wVectors, // wave vectors (same units as the pixels array)
contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
x0, // center coordinates
y0,
title, // title base for optional plots names
this.debugLevel);
/*
return correlationContrast (
pixels, // square pixel array
widowedGreens,
wVectors, // wave vectors (same units as the pixels array)
// ringWidth, // ring (around r=0.5 dist to opposite corr) width
contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5
contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (in PIXELS), 2.0
contrastSelectSigmaOther, // Gaussian sigma to select correlation off-centers centers (fraction of UV period), 0.1
x0, // center coordinates
y0,
title, // title base for optional plots names
this.debugLevel);
*/
}
public double correlationContrastOld ( double [] pixels, // square pixel array
double [][] wVectors, // wave vectors (same units as the pixels array)
......@@ -1232,17 +1218,19 @@ public class MatchSimulatedPattern {
public double [] correlationContrast (
double [] pixels, // square pixel array
// double [] widowedGreens, // array to normailze correlation result
double [][] wVectors, // wave vectors (same units as the pixels array)
double sigma,
double sigma_center, // GGaussian sigma to select correlation centers (in PIXELS), 1.5
double sigma_other, // Gaussian sigma to select correlation off-centers centers (fraction of UV period), 0.1
double x0, // center coordinates
double y0,
String title, // title base for optional plots names
int debugLevel){
double [] badContrasts={-1.0,-1.0};
double sigma32=9*sigma*sigma;
double k=-0.5/(sigma*sigma);
double [][] sampleCentersXY={{0.0,0.0},{0.25,0.25},{0.25,-0.20},{-0.25,0.25},{-0.25,-0.25}};
double sigma32_center=9*sigma_center*sigma_center; // in pixels
double k_center=-0.5/(sigma_center*sigma_center); // in pixels
double sigma32_other=9*sigma_other*sigma_other; // in periods
double k_other=-0.5/(sigma_other*sigma_other); // in periods
double [][] sampleCentersXY={{0.0,0.0},{0.25,0.25},{0.25,-0.25},{-0.25,0.25},{-0.25,-0.25}};
int [] sampleTypes = {0,1,1,1,1};
int size=(int) Math.sqrt(pixels.length);
double [] xy= new double [2];
......@@ -1254,7 +1242,7 @@ public class MatchSimulatedPattern {
for (int n=0;n<dbgMask.length;n++) dbgMask[n]=0.0;
double [] s={0.0,0.0};
double [] w={0.0,0.0};
// double [] dbg_weights = new double [size*size];
for (i=0;i<size;i++) {
xy[1]=i-size/2-y0;
for (j=0;j<size;j++) {
......@@ -1262,16 +1250,29 @@ public class MatchSimulatedPattern {
xy[0]=j-size/2-x0;
uv=matrix2x2_mul(wVectors,xy);
for (int np=0;np<sampleCentersXY.length;np++){
double dx=uv[0]-sampleCentersXY[np][0];
double dy=uv[1]-sampleCentersXY[np][1];
r2=dx*dx+dy*dy;
if (r2<sigma32){
double m=Math.exp(k*r2);
dbgMask[index]+=m;
w[sampleTypes[np]]+=m;
double d=m*pixels[index];
if (sampleTypes[np]>0)d*=pixels[index]; // squared
s[sampleTypes[np]]+=d;
if (sampleTypes[np] == 0) { // center spot, size in pixels
r2 = xy[0]*xy[0] + xy[1]*xy[1];
if (r2 < sigma32_center){
double m=Math.exp(k_center*r2);
dbgMask[index]+=m;
w[sampleTypes[np]]+=m;
double d=m*pixels[index];
if (sampleTypes[np]>0) d *= pixels[index]; // squared
s[sampleTypes[np]]+=d;
}
} else { // between correlation spots, size relative to the periods
double dx=uv[0]-sampleCentersXY[np][0];
double dy=uv[1]-sampleCentersXY[np][1];
r2=dx*dx+dy*dy;
if (r2 < sigma32_other){
double m=Math.exp(k_other*r2);
dbgMask[index]+=m;
w[sampleTypes[np]]+=m;
double d=m*pixels[index];
if (sampleTypes[np]>0) d*=pixels[index]; // squared
s[sampleTypes[np]]+=d;
}
}
}
}
......@@ -1280,6 +1281,7 @@ public class MatchSimulatedPattern {
if (debugLevel>1) System.out.println("Not enough data for correlation contrast: center - w[0]="+w[0]+" opposite - w[1]="+w[1]);
return badContrasts;
}
double [][] dbg_corr_mask = {pixels, dbgMask};
double aCenter= s[0]/w[0];
double aQuiet=Math.sqrt(s[1]/w[1]);
double rContrast=aCenter/aQuiet;
......@@ -2086,228 +2088,7 @@ public class MatchSimulatedPattern {
double [] checker_phases= findCheckerPhases(dhp, max_phases); /* may be different for greens==true . No, the same */
for (int i=0;i<2;i++) rslt[i][2]=checker_phases[i];
if (this.debugLevel > (debug_threshold + 0)) System.out.println();
if (this.debugLevel < 1000) return rslt;
// below is dead (older) code
double [] pixels=input_pixels.clone();
double [][]result=new double [2][3];
//System.out.println("pixels.length="+pixels.length); //4096
ImageProcessor ip, ip1;
FHT fht, fht1;
double[][][] fft_complex,fft_corr;
double[][] fft_gamma;
int i,j;
double DCLevel=0.0;
double a;
float []floatPixels=new float[pixels.length];
for (i=0;i<pixels.length; i++) DCLevel+=pixels[i];
DCLevel/=(size*size);
for (i=0;i<pixels.length; i++) pixels[i]-=DCLevel;
// convert to float for image processor;
for (i=0;i<pixels.length; i++) floatPixels[i]=(float) pixels[i];
ip = new FloatProcessor(size,size);
ip.setPixels(floatPixels);
if (this.debugLevel>8) {
ip.resetMinAndMax();
ImagePlus imp_direct= new ImagePlus(title+"_Direct_"+patternDetectParameters.corrGamma, ip);
imp_direct.show();
}
fht = new FHT(ip);
// Swapping quadrants, so the center will be 0,0
fht.swapQuadrants();
// get to frequency domain
fht.transform();
if (this.debugLevel>5) {
floatPixels=(float []) fht.getPixels();
ImageProcessor ip_fht = new FloatProcessor(size,size);
ip_fht.setPixels(floatPixels);
ip_fht.resetMinAndMax();
ImagePlus imp_fht= new ImagePlus(title+"_FHT", ip_fht);
imp_fht.show();
}
// Convert from FHT to complex FFT
fft_complex= FHT2FFTHalf (fht,size);
if (this.debugLevel>7) {
(new ShowDoubleFloatArrays()).showComplex(fft_complex,"fft_complex");
}
// will need fft_complex again later for later phase pattern measurements, calculate fft_gamma for correlation (pattern 2 frequencies measurement)
fft_gamma=new double [size][size];
floatPixels=new float[pixels.length];
DCLevel=0.0;
for (i=0;i<fft_complex.length; i++) for (j=0;j<fft_complex[0].length;j++) {
fft_gamma[i][j]=Math.pow(fft_complex[i][j][0]*fft_complex[i][j][0]+fft_complex[i][j][1]*fft_complex[i][j][1],patternDetectParameters.corrGamma);
DCLevel+=fft_gamma[i][j];
floatPixels[i*size+j]=(float) fft_gamma[i][j];
}
DCLevel/=(fft_complex.length*fft_complex[0].length);
for (i=0;i<fft_complex.length; i++) for (j=0;j<fft_complex[0].length;j++) {
floatPixels[i*size+j]-=DCLevel;
if ((i>0)&& (i<(size/2))){
floatPixels[(size-i)*size+((size-j)%size)]=floatPixels[i*size+j];
}
}
/* TODO: maybe it is better to find the pattern frequencies just here, without converting back.
After rejecting low frequencies, there seem to be just 2 nice maximums - easy to extract*/
// now perform direct FFT of gamma(power spectrum)
ip1 = new FloatProcessor(size,size);
ip1.setPixels(floatPixels);
if (this.debugLevel>7) {
ip1.resetMinAndMax();
ImagePlus imp1= new ImagePlus(title+"_gamma(ps)_"+patternDetectParameters.corrGamma, ip1);
imp1.show();
}
fht1 = new FHT(ip1);
// Swapping quadrants, so the center will be 0,0
fht1.swapQuadrants();
fht1.transform();
fft_corr= FHT2FFTHalf (fht1,size);
if (this.debugLevel>7) {
(new ShowDoubleFloatArrays()).showComplex(fft_corr,"fft_corr");
}
double[] highPassFilter=new double[fft_complex[0].length];
double expK=(patternDetectParameters.corrSigma>0)?(1.0/(2*patternDetectParameters.corrSigma*patternDetectParameters.corrSigma)):0.0;
for (j=0;j<=fft_complex[0].length/2;j++) {
highPassFilter[j]=(expK>0.0)?(1.0-Math.exp(-(expK*j*j))):1.0;
if (j>0) highPassFilter[highPassFilter.length-j]=highPassFilter[j];
}
for (i=0;i<fft_complex.length; i++) for (j=0;j<fft_complex[0].length;j++) {
fft_corr[i][j][0]=highPassFilter[i]*highPassFilter[j]*(fft_corr[i][j][0]*fft_corr[i][j][0]+fft_corr[i][j][1]*fft_corr[i][j][1]);
fft_corr[i][j][1]=0.0;
}
if (this.debugLevel>7) {
(new ShowDoubleFloatArrays()).showComplex(fft_corr,"fft_corr-high_pass");
}
// Convert fft array back to fht array and
// set fht_target pixels with new values
fht1.setPixels (floatFFTHalf2FHT (fft_corr,size)); /* FIXME: - done, there is no difference as Im()==0 */
/// optionally show the result
if (this.debugLevel>7) {
ImageProcessor ip_fht2 = new FloatProcessor(size,size);
ip_fht2.setPixels(floatFFTHalf2FHT (fft_corr,size));
ip_fht2.resetMinAndMax();
ImagePlus imp_fht2= new ImagePlus(title+"_fht_corr_"+patternDetectParameters.corrGamma, ip_fht2);
imp_fht2.show();
}
/// transform to space
fht1.inverseTransform();
floatPixels=(float []) fht1.getPixels();
a=1/floatPixels[0];
for (i=0; i<floatPixels.length; i++){
floatPixels[i]*=a;
}
fht1.setPixels(floatPixels);
//System.out.println("2:y="+y+" x="+x+" base_b="+base_b+" base="+base);
fht1.swapQuadrants();
if (this.debugLevel>2) {
fht1.resetMinAndMax();
ImagePlus imp_corr= new ImagePlus(title+"_corr_"+patternDetectParameters.corrGamma, fht1);
imp_corr.show();
}
// return direct_target;
floatPixels =(float[])fht1.getPixels();
for (i=0;i<floatPixels.length;i++) pixels[i]=floatPixels[i];
int [][] max2OnSpectrum= findFirst2MaxOnSpectrum (fft_complex, // complex, top half, starting from 0,0
1, // skip +- from (0,0) and previous max - add parameter to dialog?
0.5); // 0.5 - 30deg. orthogonality of 2 vectors - 1.0 - perpendicular, 0.0 - parallel - add parameter to dialog?
/**TODO: get out on failure */
if (max2OnSpectrum==null) {
if (this.debugLevel>2){
System.out.println("findPattern() 1: Failed to find a pattern");
if (this.debugLevel>2){
SDFA_INSTANCE.showArrays(input_pixels, "failed-findPattern-1-");
}
}
return null;
}
/* Trying to filter out unreasonable maximums (if there is no pattern at all) */
double maxFrequency=0.25*fft_complex.length;
if ((Math.abs(max2OnSpectrum[0][0])>maxFrequency) ||
(Math.abs(max2OnSpectrum[0][1])>maxFrequency) ||
(Math.abs(max2OnSpectrum[1][0])>maxFrequency) ||
(Math.abs(max2OnSpectrum[1][1])>maxFrequency)) {
if (this.debugLevel>2) {
System.out.println("Failed to detect pattern, as frequecy is above limit="+IJ.d2s(maxFrequency,2));
System.out.println("Maximum 1 on spectrum: x="+IJ.d2s(max2OnSpectrum[0][0],4)+" y="+IJ.d2s(max2OnSpectrum[0][1],4));
System.out.println("Maximum 2 on spectrum: x="+IJ.d2s(max2OnSpectrum[1][0],4)+" y="+IJ.d2s(max2OnSpectrum[1][1],4));
}
return null;
}
if (this.debugLevel>6) {
System.out.println("Maximum 1 on spectrum: x="+IJ.d2s(max2OnSpectrum[0][0],4)+" y="+IJ.d2s(max2OnSpectrum[0][1],4));
System.out.println("Maximum 2 on spectrum: x="+IJ.d2s(max2OnSpectrum[1][0],4)+" y="+IJ.d2s(max2OnSpectrum[1][1],4));
}
int [][] startPoints={{max2OnSpectrum[0][0]+max2OnSpectrum[1][0],
max2OnSpectrum[0][1]+max2OnSpectrum[1][1]},
{max2OnSpectrum[0][0]-max2OnSpectrum[1][0],
max2OnSpectrum[0][1]-max2OnSpectrum[1][1]}};
if (startPoints[1][1] <0) { /* startPoints[1][1] > 0 anyway */
startPoints[1][0]= -startPoints[1][0];
startPoints[1][1]= -startPoints[1][1];
}
if (this.debugLevel>2) {
System.out.println("Predicted correlation maximum 1 from spectrum: x="+IJ.d2s(startPoints[0][0],4)+" y="+IJ.d2s(startPoints[0][1],4));
System.out.println("Predicted correlation maximum 2 from spectrum: x="+IJ.d2s(startPoints[1][0],4)+" y="+IJ.d2s(startPoints[1][1],4));
}
double[][] max2= findFirst2MaxOnCorrelation(
pixels,
startPoints,
patternDetectParameters
);
/**TODO: get out on failure */
if (max2==null) {
if (this.debugLevel>2){
System.out.println("findPattern() 2: Failed to find a pattern");
if (this.debugLevel>2){
SDFA_INSTANCE.showArrays(input_pixels, "failed-findPattern-2-");
}
}
return null;
}
/* these are combined greens, convert vectors to original pixel space)! */
if (greens) {
double [][] rotMatrix= {{1.0,-1.0},{1.0,1.0}};
double [][] max2orig= matrix2x2_mul(max2,rotMatrix);
for (i=0;i<2;i++) for (j=0;j<2;j++) result[i][j]=max2orig[i][j]; // result is [2][3], max2orig is [2][2]
if (this.debugLevel>2) {
System.out.println("Corrected to original pixels[0] x="+IJ.d2s(result[0][0],4)+" y="+IJ.d2s(result[0][1],4));
System.out.println("Corrected to original pixels[1] x="+IJ.d2s(result[1][0],4)+" y="+IJ.d2s(result[1][1],4));
}
} else {
for (i=0;i<2;i++) for (j=0;j<2;j++) result[i][j]=max2[i][j]; // result is [2][3], max2 is [2][2]
}
/* Calculate locations of the maximums on FFT (corresponding to the diagonals of the checkerboard pattern) */
double [][] maxOnFFT = {{2*size*(max2[0][0]-max2[1][0]),2*size*(max2[0][1]-max2[1][1])},
{2*size*(max2[0][0]+max2[1][0]),2*size*(max2[0][1]+max2[1][1])}};
/* We have only one half of the FFT data so rotate 180-degrees around the center if the point is in the bottom half*/
double [] maxPhases = getPatternPhasesFromFFT(fft_complex, size, maxOnFFT);
double [] checkerPhases= findCheckerPhases(max2, maxPhases); /* may be different for greens==true . No, the same */
for (i=0;i<2;i++) result[i][2]=checkerPhases[i];
if (this.debugLevel>2) System.out.println();
return result;
return rslt;
}
/* ======================================================================== */
// calculate pattern 3D phases by interpolating im/re for the found maximums
......@@ -3715,7 +3496,7 @@ public class MatchSimulatedPattern {
String dbgStr
){
this.debugLevel = 3;
// this.debugLevel = 3;
int debug_threshold = 2;
......@@ -4254,7 +4035,7 @@ public class MatchSimulatedPattern {
node[2]);
waveFrontList.clear();
putInWaveList(waveFrontList, centerUV, 0);
if (global_debug_level>1) {
if (global_debug_level>0) { //1) {
System.out.println("putInWaveList(waveFrontList, {"+centerUV[0]+","+centerUV[1]+"}, 0);");
}
}
......@@ -4492,7 +4273,7 @@ public class MatchSimulatedPattern {
wv[0], //null, // double [] wv1,
wv[1]); //null); // double [] wv2);
if (cleanup.get()) addedCells.getAndIncrement();
if (debugLevel>debugThreshold) {
if (debugLevel>debugThreshold-2) { //was no "-2"
dbgStr+="==>added"+iUVdir[0]+"/"+iUVdir[1]+", dir"+iUVdir[2];
System.out.println(dbgStr);
}
......@@ -4720,6 +4501,18 @@ public class MatchSimulatedPattern {
) {
return numDefinedCells;
}
if ( (numDefinedCells < distortionParameters.minimalPatternCluster) &&
(numDefinedCells > 10)) // detected enough cells
{
if (global_debug_level > -1) {
System.out.println("***** Initial cluster has "+numDefinedCells+ " cells that is less than "+
"distortionParameters.minimalPatternCluster = "+distortionParameters.minimalPatternCluster+
" *****");
}
// return numDefinedCells;
}
if (roi!=null){ // don't use this feature with ROI as it can be small
if (global_debug_level>0) System.out.println("Initial pattern cluster is small ("+numDefinedCells+"), but ROI is set - no retries");
{
......@@ -4912,7 +4705,7 @@ public class MatchSimulatedPattern {
final boolean updateStatus,
final int debugLevel
){
final int debugThreshold=-1; // 1; ** Restore 1
final int debugThreshold=1; // -1; // 1; ** Restore 1
if ((debugLevel>debugThreshold) && ((debugLevel>1) || (startScanIndex>3))) {
int debugNumLeft=0;
for (boolean b:triedIndices) if (!b) debugNumLeft++;
......@@ -4981,7 +4774,7 @@ public class MatchSimulatedPattern {
);
if ((node!=null) && (node[0]!=null)) {
nodeQueue.add(new GridNode(node));
if (debugLevel>debugThreshold) System.out.println("adding candidate "+n+" x0="+point[0]+" y0="+point[1]+" -> "+ node[0][0]+"/"+node[0][1]+" seqNumber.get()="+seqNumber.get()+" n="+n);
if (debugLevel>debugThreshold-1) System.out.println("adding candidate "+n+" x0="+point[0]+" y0="+point[1]+" -> "+ node[0][0]+"/"+node[0][1]+" seqNumber.get()="+seqNumber.get()+" n="+n);
}
} else {
if (debugLevel>debugThreshold) System.out.println("-----"+debugNumThread+":"+n+", nv="+nv+", nh="+nh);
......@@ -7944,14 +7737,16 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
* fourth slice - target V (may be negative)
* other slices - if present
* fifth slice - local grid contrast (looks for 2 white and 2 blacks around) - can be used to filter
* sixth slice - red intensity of the grid (avaraged around the grid node)
* seventh slice - green intensity of the grid (avaraged around the grid node)
* eighth slice - blue intensity of the grid (avaraged around the grid node)
* sixth slice - red intensity of the grid (averaged around the grid node)
* seventh slice - green intensity of the grid (averaged around the grid node)
* eighth slice - blue intensity of the grid (averaged around the grid node)
*/
public ImagePlus getCalibratedPatternAsImage(String title, int numUsedPointers){
if ((this.targetUV==null) ||(this.pXYUV==null)) {
System.out.println("getCalibratedPatternAsImage(): this.targetUV="+((this.targetUV==null)?"null":"not null")+", this.pixelsUV="+((this.pXYUV==null)?"null":"not null"));
return null;
System.out.println("Using grid w/o absolute calibration.");
unCalibrateGrid();
// return null;
}
int numSlices=(this.gridContrastBrightness==null)?4:8;
float [][] pixels=new float [numSlices][getWidth()*getHeight()];
......@@ -8125,8 +7920,13 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
public ImagePlus getCalibratedPatternAsImage(
ImagePlus imp_src,
String prefix, int numUsedPointers){
// ImagePlus imp_result=getCalibratedPatternAsImage("grid-"+imp_src.getTitle(), numUsedPointers);
// ImagePlus imp_result=getCalibratedPatternAsImage("grid-"+imp_src.getTitle(), numUsedPointers);
ImagePlus imp_result=getCalibratedPatternAsImage(prefix+imp_src.getTitle(), numUsedPointers);
if (imp_result == null) {
System.out.println("getCalibratedPatternAsImage(): Grid is empty !");
return null;
}
// copy all the properties to the new image
JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
jp4_instance.copyProperties (imp_src,imp_result);
......@@ -9023,8 +8823,8 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
greens,
WVgreens, // wave vectors (same units as the pixels array)
// distortionParameters.correlationRingWidth, // ring (around r=0.5 dist to opposite corr) width
distortionParameters.contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (pixels, 2.0)
distortionParameters.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
distortionParameters.contrastAverageSigma,
//TODO: verify that displacement is correct here (sign, direction)
centerXY[0], // x0, // center coordinates
centerXY[1], //y0,
......@@ -9109,7 +8909,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
int debug_level,
String dbgStr
){
int debug_threshold = 2;
int debug_threshold = 3;
// next print - same for good and bad, correction==null
if (dbgStr!=null) System.out.println(dbgStr+ ": wv0x="+wv0x+" wv0y="+wv0y+ " wv1x="+wv1x+" wv1y="+wv1y+
" beforeXY[0]="+beforeXY[0]+", beforeXY[1]="+beforeXY[1]+" correction is "+((correction==null)?"null":"not null"));
......@@ -9118,12 +8918,11 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
boolean dbgThis=
(Math.abs(beforeXY[0]-patternDetectParameters.debugX)<patternDetectParameters.debugRadius) &&
(Math.abs(beforeXY[1]-patternDetectParameters.debugY)<patternDetectParameters.debugRadius);
dbgThis=true;
//dbgThis=true;
if (dbgThis) {
System.out.println("correctedPatternCrossLocationAverage4(), beforeXY[0]="+beforeXY[0]+", beforeXY[1]="+beforeXY[1]);
debug_level+=3;
}
// System.out.println("correctedPatternCrossLocationAverage4(): beforeXY[0]="+beforeXY[0]+". beforeXY[1]="+beforeXY[1]);
// Just for testing
beforeXY[0]+=distortionParameters.correlationDx; // offset, X (in pixels)
beforeXY[1]+=distortionParameters.correlationDy; // offset y (in pixels)
......@@ -9203,18 +9002,6 @@ dbgThis=true;
}
}
/*
if ((min_span<uv_threshold) && (window2!=null)) { // trying to increase only twice
thisCorrelationSize*=2;
min_span*=2;
thisWindow=window2;
if ((min_span<uv_threshold) && (window4!=null)) {
thisCorrelationSize*=2;
min_span*=2;
thisWindow=window4;
}
}
*/
setCorrelationSizesUsed(thisCorrelationSize);
if ((debug_level > (debug_threshold - 2))&&(thisCorrelationSize>distortionParameters.correlationSize)) System.out.println("**** u/v span too small, increasing FFT size to "+thisCorrelationSize);
Rectangle centerCross=correlationSelection(
......@@ -9263,7 +9050,6 @@ dbgThis=true;
}
double [][] modelCorrs= new double[numOfNeib][];
double [][] modelCorrs_new= new double[numOfNeib][];
double [][] debugGreens=new double[numOfNeib][0];
for (numNeib=0;numNeib<numOfNeib;numNeib++) {
neibCenter[0]=diffBeforeXY[0]+0.5*(greenNeib[numNeib][0]+greenNeib[numNeib][1]);
......@@ -9309,8 +9095,358 @@ dbgThis=true;
debugGreens[numNeib]=simGreensCentered.clone();
// testing if phase reversal would exactly inverse result pattern - tested, perfect
double [] simGreensCenteredClone = simGreensCentered.clone();
modelCorrs[numNeib]=fht_instance.phaseCorrelate (
greens.clone(),
simGreensCentered,
patternDetectParameters.phaseCoeff,
0,// distortionParameters.correlationHighPassSigma,
patternDetectParameters.lowpass_sigma, // (fast?distortionParameters.correlationLowPassSigma:0.0),// moved to decimation via FFT
null,
null);
if (dbgStr!=null) {
double dbgSumWindow=0.0;
for (double[] dbgSlice:modelCorrs) for (double dbgD:dbgSlice) dbgSumWindow+=dbgD;
System.out.println(dbgStr+ ": SUM of modelCorrs="+dbgSumWindow);
}
}
if (debug_level > (debug_threshold + 0)){
System.out.println(">=========Showing simGreensCentered"+ixc+":"+iyc);
SDFA_INSTANCE.showArrays(debugGreens, true, "simGreensCentered"+ixc+":"+iyc);
}
if (debug_level > (debug_threshold + 0)){
System.out.println(">=========Showing modelCorrs, passNumber="+passNumber);
SDFA_INSTANCE.showArrays(modelCorrs, true, "modelCorrs:"+numOfNeib);
}
// combine 4 correlations into the double resolution, same output size (so half input size) array
int halfSize=thisCorrelationSize/2;
int qSize=thisCorrelationSize/4;
int thisFFTSubdiv=distortionParameters.correlationFFTSubdiv;
double thisLowpass=distortionParameters.correlationLowPassSigma;
double [] modelCorr;
if (numOfNeib>1) {
modelCorr=new double [thisCorrelationSize*thisCorrelationSize];
for (int i=0;i<modelCorr.length; i++) modelCorr[i]=0.0;
for (int dy=0;dy<2;dy++) for (int dx=0;dx<2;dx++) {
for (int y=0;y<halfSize;y++) for (int x=0;x<halfSize;x++) {
modelCorr[(2*y+dy)*thisCorrelationSize+(2*x+dx)]+=
modelCorrs[2*dy+dx][(qSize+y)*thisCorrelationSize+(qSize+x)];
}
}
thisLowpass/=2.0; // the lower the value, the more filtering. Decimated twice,so low pass filtering - accordingly
thisFFTSubdiv=(thisFFTSubdiv>1)?(thisFFTSubdiv/2):1;
} else {
modelCorr= modelCorrs[0]; // also - different size
}
if (debug_level > (debug_threshold + 0)){
System.out.println(">==========Showing modelCorr");
SDFA_INSTANCE.showArrays(modelCorr, thisCorrelationSize,thisCorrelationSize, "modelCorr");
}
if (fast) centerXY= correlationMaximum( // maybe twice actual size if
modelCorr,
distortionParameters.correlationMaxOffset,
(debug_level > (debug_threshold + 0)) && (numNeib==0)); // low-pass filtering should already be done
else centerXY= correlationMaximum(
modelCorr,
distortionParameters.correlationRadius,
distortionParameters.correlationThreshold, //double threshold, // fraction of maximum (slightly less than 1.0) to limit the top part of the maximum for centroid
distortionParameters.correlationSubdiv,
thisFFTSubdiv,
fht_instance,
distortionParameters.correlationMaxOffset,
thisLowpass, //distortionParameters.correlationLowPassSigma
// (debug_level>2) && (passNumber>1));
(debug_level > (debug_threshold + 0)));
if (centerXY==null) {
if (debug_level > (debug_threshold - 1)) System.out.println("Too far from the center01 ("+beforeXY[0]+"/"+beforeXY[1]+")");
if (dbgStr!=null) System.out.println(dbgStr+ "- Too far from the center01 ("+beforeXY[0]+"/"+beforeXY[1]+")");
return null;
}
if (numNeib>1){
centerXY[0]*=0.5;
centerXY[1]*=0.5;
for (int i=0;i<2;i++) for (int j=0;j<2;j++) WVgreens[i][j]*=0.5;
}
double [] contrasts= correlationContrast(
modelCorr,
greens,
WVgreens, // wave vectors (same units as the pixels array)
distortionParameters.contrastSelectSigmaCenter, // Gaussian sigma to select correlation (pixels, 2.0)
distortionParameters.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
centerXY[0], // x0, // center coordinates
centerXY[1], //y0,
"test-contrast"); // title base for optional plots names
if ((debug_level > (debug_threshold - 1))) {
System.out.println("contrast = "+contrasts[0]);
}
contrast=contrasts[0];
result[2]=contrast;
if (Double.isNaN(contrasts[0]) || ((distortionParameters.correlationMinContrast>0) && (contrasts[0]<distortionParameters.correlationMinContrast))) {
if ((debug_level > (debug_threshold - 1))) System.out.println("Contrast too low - "+contrasts[0]+"<"+distortionParameters.correlationMinContrast);
if (debug_level > (debug_threshold - 1)) System.out.println("Contrast "+IJ.d2s(contrasts[0],3)+" ("+distortionParameters.correlationMinContrast+")"+
" is TOO LOW ("+IJ.d2s(beforeXY[0],3)+"/"+IJ.d2s(beforeXY[1],3)+")->"+
IJ.d2s(centerXY[0],3)+"/"+IJ.d2s(centerXY[1],3));
if (dbgStr!=null) System.out.println(dbgStr+ " - Contrast "+IJ.d2s(contrasts[0],3)+" ("+distortionParameters.correlationMinContrast+")"+
" is TOO LOW ("+IJ.d2s(beforeXY[0],3)+"/"+IJ.d2s(beforeXY[1],3)+")->"+
IJ.d2s(centerXY[0],3)+"/"+IJ.d2s(centerXY[1],3));
return null;
} else {
if (debug_level > (debug_threshold - 1)) System.out.println("Contrast "+IJ.d2s(contrasts[0],3)+" ("+distortionParameters.correlationMinContrast+")"+
" is GOOD ("+IJ.d2s(beforeXY[0],3)+"/"+IJ.d2s(beforeXY[1],3)+")->"+
IJ.d2s(centerXY[0],3)+"/"+IJ.d2s(centerXY[1],3));
if (dbgStr!=null) System.out.println(dbgStr+ " - Contrast "+IJ.d2s(contrasts[0],3)+" ("+distortionParameters.correlationMinContrast+")"+
" is GOOD ("+IJ.d2s(beforeXY[0],3)+"/"+IJ.d2s(beforeXY[1],3)+")->"+
IJ.d2s(centerXY[0],3)+"/"+IJ.d2s(centerXY[1],3));
}
if (Double.isNaN(contrasts[1]) || ((distortionParameters.correlationMinAbsoluteContrast>0) && (contrasts[1]<distortionParameters.correlationMinAbsoluteContrast))) {
if (debug_level > (debug_threshold - 1)) System.out.println("Absolute contrast too low - "+contrasts[1]+"<"+distortionParameters.correlationMinAbsoluteContrast);
if (debug_level > (debug_threshold - 1)) System.out.println("Absolute contrast "+IJ.d2s(contrasts[1],3)+" ("+distortionParameters.correlationMinAbsoluteContrast+")"+
" is too low ("+IJ.d2s(beforeXY[0],3)+"/"+IJ.d2s(beforeXY[1],3)+")->"+
IJ.d2s(centerXY[0],3)+"/"+IJ.d2s(centerXY[1],3));
if (dbgStr!=null) System.out.println(dbgStr+ " - Absolute contrast "+IJ.d2s(contrasts[1],3)+" ("+distortionParameters.correlationMinAbsoluteContrast+")"+
" is too low ("+IJ.d2s(beforeXY[0],3)+"/"+IJ.d2s(beforeXY[1],3)+")->"+
IJ.d2s(centerXY[0],3)+"/"+IJ.d2s(centerXY[1],3));
return null;
} else {
if (dbgStr!=null) System.out.println(dbgStr+ " - Absolute contrast "+IJ.d2s(contrasts[1],3)+" ("+distortionParameters.correlationMinAbsoluteContrast+")"+
" is GOOD ("+IJ.d2s(beforeXY[0],3)+"/"+IJ.d2s(beforeXY[1],3)+")->"+
IJ.d2s(centerXY[0],3)+"/"+IJ.d2s(centerXY[1],3));
}
if (debug_level > (debug_threshold - 3))System.out.println(">>>Contrast="+contrasts[0]+"/"+contrasts[1]+" ("+IJ.d2s(beforeXY[0],3)+":"+IJ.d2s(beforeXY[1],3)+")->"+IJ.d2s(result[0],3)+":"+IJ.d2s(result[1],3));
result[0]=ixc-(-centerXY[0]-centerXY[1])+diffBeforeXY[0];
result[1]=iyc-( centerXY[0]-centerXY[1])+diffBeforeXY[1];
if (debug_level > (debug_threshold + 0)) System.out.println(">---correctedPatternCrossLocation: before x="+IJ.d2s(beforeXY[0],3)+" y="+IJ.d2s(beforeXY[1],3));
if (debug_level > (debug_threshold + 0)) System.out.println(">+++correctedPatternCrossLocation: after x="+IJ.d2s(result[0],3)+" y="+IJ.d2s(result[1],3));
return result;
}
private double [] correctedPatternCrossLocationAverage4TestOldNew(
double [] beforeXY, // initial coordinates of the pattern cross point
double wv0x,
double wv0y,
double wv1x,
double wv1y,
double [][] correction,
ImagePlus imp, // image data (Bayer mosaic)
DistortionParameters distortionParameters, //distortionParameters.refineCorrelations
MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
MatchSimulatedPattern matchSimulatedPattern, // correlationSize
SimulationPattern.SimulParameters thisSimulParameters,
boolean equalizeGreens,
double [] window, // window function
double [] window2, // window function - twice FFT size (or null)
double [] window4, // window function - 4x FFT size (or null)
SimulationPattern simulationPattern,
boolean negative, // invert cross phase
DoubleFHT fht_instance,
boolean fast, // use fast measuring of the maximum on the correlation
double [][] locsNeib, // locations and weights of neighbors to average
int debug_level,
String dbgStr
){
int debug_threshold = 3;
// next print - same for good and bad, correction==null
if (dbgStr!=null) System.out.println(dbgStr+ ": wv0x="+wv0x+" wv0y="+wv0y+ " wv1x="+wv1x+" wv1y="+wv1y+
" beforeXY[0]="+beforeXY[0]+", beforeXY[1]="+beforeXY[1]+" correction is "+((correction==null)?"null":"not null"));
boolean dbgThis=
(Math.abs(beforeXY[0]-patternDetectParameters.debugX)<patternDetectParameters.debugRadius) &&
(Math.abs(beforeXY[1]-patternDetectParameters.debugY)<patternDetectParameters.debugRadius);
dbgThis=true;
if (dbgThis) {
System.out.println("correctedPatternCrossLocationAverage4(), beforeXY[0]="+beforeXY[0]+", beforeXY[1]="+beforeXY[1]);
debug_level+=3;
}
// System.out.println("correctedPatternCrossLocationAverage4(): beforeXY[0]="+beforeXY[0]+". beforeXY[1]="+beforeXY[1]);
// Just for testing
beforeXY[0]+=distortionParameters.correlationDx; // offset, X (in pixels)
beforeXY[1]+=distortionParameters.correlationDy; // offset y (in pixels)
double [][] convMatrix= {{1.0,-1.0},{1.0,1.0}}; // from greens2 to pixel WV
double [][] invConvMatrix= matrix2x2_scale(matrix2x2_invert(convMatrix),2.0);
double [] result=new double [3];
result[0]=beforeXY[0];
result[1]=beforeXY[1];
result[2]=0.0; // contrast
if (fht_instance==null) fht_instance=new DoubleFHT(); // move upstream to reduce number of initializations
//create diagonal green selection around ixc,iyc
double [][]wv={{wv0x, wv0y},
{wv1x, wv1y}};
double [][] WVgreens=matrix2x2_mul(wv,invConvMatrix);
if (debug_level > debug_threshold) System.out.println("WVgreens[0][0]="+IJ.d2s(WVgreens[0][0],3)+
" WVgreens[0][1]="+IJ.d2s(WVgreens[0][1],3)+
" WVgreens[1][0]="+IJ.d2s(WVgreens[1][0],3)+
" WVgreens[1][1]="+IJ.d2s(WVgreens[1][1],3));
double [] dUV;
double[][] sim_pix;
double [] simGreensCentered;
// double [] modelCorr;
double [] centerXY;
double contrast;
int numNeib;
double []corr=null;
double [] neibCenter=new double[2];
if (correction!=null) { // overwrite wave vectors
wv[0][0]=correction[0][0];
wv[0][1]=correction[0][1];
wv[1][0]=correction[1][0];
wv[1][1]=correction[1][1];
if (correction[0].length>3) { // enough data for quadratic approximation
corr=new double[10];
corr[0]=correction[0][3]/4;
corr[1]=correction[0][4]/4;
corr[2]=correction[0][5]/4;
corr[3]=correction[1][3]/4;
corr[4]=correction[1][4]/4;
corr[5]=correction[1][5]/4;
corr[6]=0.0;
corr[7]=0.0;
corr[9]=0.0;
corr[9]=0.0;
}
}
double u_span=Math.sqrt(wv0x*wv0x+wv0y*wv0y)*distortionParameters.correlationSize;
double v_span=Math.sqrt(wv1x*wv1x+wv1y*wv1y)*distortionParameters.correlationSize;
double min_span=Math.min(u_span, v_span);
int thisCorrelationSize=distortionParameters.correlationSize;
double [] thisWindow=window;
double uv_threshold=distortionParameters.minUVSpan*0.25*Math.sqrt(2.0);
if (
(min_span<uv_threshold) &&
(window2!=null) &&
(thisCorrelationSize<distortionParameters.maximalCorrelationSize)) { // trying to increase only twice
thisCorrelationSize*=2;
min_span*=2;
thisWindow=window2;
if (
(min_span<uv_threshold) &&
(window4!=null) &&
(thisCorrelationSize<distortionParameters.maximalCorrelationSize)) {
thisCorrelationSize*=2;
min_span*=2;
thisWindow=window4;
}
}
setCorrelationSizesUsed(thisCorrelationSize);
if ((debug_level > (debug_threshold - 2))&&(thisCorrelationSize>distortionParameters.correlationSize)) System.out.println("**** u/v span too small, increasing FFT size to "+thisCorrelationSize);
Rectangle centerCross=correlationSelection(
beforeXY, // initial coordinates of the pattern cross point
thisCorrelationSize);
int ixc=centerCross.x+centerCross.width/2;
int iyc=centerCross.y+centerCross.height/2;
double [] diffBeforeXY={beforeXY[0]-ixc, beforeXY[1]-iyc};
double[][] input_bayer=splitBayer (imp,centerCross,equalizeGreens);
if (debug_level > (debug_threshold +1)) SDFA_INSTANCE.showArrays(input_bayer, true, "centered");
if (debug_level > (debug_threshold +0)) SDFA_INSTANCE.showArrays(input_bayer[4], "greens");
if (debug_level > (debug_threshold +0)) System.out.println("ixc="+ixc+" iyc="+iyc);
double [] greens=normalizeAndWindow (input_bayer[4], thisWindow);
if (debug_level > (debug_threshold +0)) SDFA_INSTANCE.showArrays(greens, "greensWindowed");
// average is not zero - probably
if (debug_level > (debug_threshold + 0)) {
System.out.println(" wv0x="+IJ.d2s(wv0x,5)+" wv0y="+IJ.d2s(wv0y,5));
System.out.println(" wv1x="+IJ.d2s(wv1x,5)+" wv1y="+IJ.d2s(wv1y,5));
System.out.println(" u-span="+IJ.d2s(u_span,3)+" v-span="+IJ.d2s(v_span,3)+" threshold="+IJ.d2s(uv_threshold,3)+" ("+IJ.d2s(distortionParameters.minUVSpan,3)+")");
if (corr!=null) {
System.out.println(" Ax="+IJ.d2s(corr[0],8)+" Bx="+IJ.d2s(corr[1],8)+" Cx="+IJ.d2s(corr[2],8)+" Dx="+IJ.d2s(corr[6],8)+" Ex="+IJ.d2s(corr[7],8));
System.out.println(" Ay="+IJ.d2s(corr[3],8)+" By="+IJ.d2s(corr[4],8)+" Cy="+IJ.d2s(corr[5],8)+" Dy="+IJ.d2s(corr[8],8)+" Ey="+IJ.d2s(corr[9],8));
}
}
int [][] greenNeib={{0,0},{0,1},{1,0},{1,1}};
int numOfNeib=distortionParameters.correlationAverageOnRefine?greenNeib.length:1;
if (debug_level > (debug_threshold + 0)) {
System.out.println(" numOfNeib="+numOfNeib+" (distortionParameters.correlationAverageOnRefine="+distortionParameters.correlationAverageOnRefine);
}
if (locsNeib.length==1) {
numOfNeib=1; // on the first pass, from legacy
if (debug_level > (debug_threshold + 0)) {
System.out.println("Reduced numOfNeib to "+numOfNeib+" as locsNeib.length="+locsNeib.length);
}
}
if (dbgStr!=null) {
double dbgSumWindow=0.0;
for (double dbgD:thisWindow) dbgSumWindow+=dbgD;
// All he same - good/bad
System.out.println(dbgStr+ ": thisCorrelationSize="+thisCorrelationSize+" min_span="+min_span+ " dbgSumWindow="+dbgSumWindow+
"locsNeib.length="+locsNeib.length+" fast="+fast+
" numOfNeib="+numOfNeib+" (distortionParameters.correlationAverageOnRefine="+distortionParameters.correlationAverageOnRefine);
}
double [][] modelCorrs= new double[numOfNeib][];
double [][] modelCorrs_new= new double[numOfNeib][];
double [][] debugGreens=new double[numOfNeib][0];
for (numNeib=0;numNeib<numOfNeib;numNeib++) {
neibCenter[0]=diffBeforeXY[0]+0.5*(greenNeib[numNeib][0]+greenNeib[numNeib][1]);
neibCenter[1]=diffBeforeXY[1]+0.5*(greenNeib[numNeib][0]-greenNeib[numNeib][1]);
dUV=matrix2x2_scale(matrix2x2_mul(wv,neibCenter),-2*Math.PI);
double [] barray= simulationPattern.simulatePatternFullPatternSafe( // Is it the most time-consuming part? should it be done once and then only extraction separate?
wv0x,
wv0y,
dUV[0]+(negative?(-Math.PI/2):Math.PI/2), // negative?(-Math.PI/2):Math.PI/2,
wv1x,
wv1y,
dUV[1]+Math.PI/2, //Math.PI/2,
corr, //null, // no mesh distortion here
thisSimulParameters.subdiv,// SIMUL.subdiv, - do not need high quality here
thisCorrelationSize,
true); // center for greens
sim_pix= simulationPattern.extractSimulPatterns (
barray,
thisSimulParameters,
1, // subdivide output pixels
thisCorrelationSize, // number of Bayer cells in width of the square selection (half number of pixels)
0,
0);
if (sim_pix==null){
System.out.println("***** BUG: extractSimulPatterns() FAILED *****");
return null;
}
if (dbgStr!=null) {
double dbgSumWindow=0.0;
for (double[] dbgSlice:sim_pix) for (double dbgD:dbgSlice) dbgSumWindow+=dbgD;
System.out.println(dbgStr+ ": SUM of sim_pix="+dbgSumWindow); // First difference good/bad
}
simGreensCentered= normalizeAndWindow (sim_pix[4], thisWindow);
if (dbgStr!=null) {
double dbgSumWindow=0.0;
for (double dbgD:simGreensCentered) dbgSumWindow+=dbgD;
System.out.println(dbgStr+ ": SUM of simGreensCentered="+dbgSumWindow);
}
debugGreens[numNeib]=simGreensCentered.clone();
// testing if phase reversal would exactly inverse result pattern - tested, perfect
double [] simGreensCenteredClone = simGreensCentered.clone();
modelCorrs[numNeib]=fht_instance.correlate (greens.clone(), // measured pixel array
// modelCorr=fht_instance.correlate (greens, // measured pixel array
......@@ -9350,32 +9486,63 @@ dbgThis=true;
// combine 4 correlations into the double resolution, same output size (so half input size) array
int halfSize=thisCorrelationSize/2;
int qSize=thisCorrelationSize/4;
double [] modelCorr;
int thisFFTSubdiv=distortionParameters.correlationFFTSubdiv;
double thisLowpass=distortionParameters.correlationLowPassSigma;
double [] modelCorr;
double [] modelCorr_new;
if (numOfNeib>1) {
modelCorr=new double [thisCorrelationSize*thisCorrelationSize];
for (int i=0;i<modelCorr.length;i++) modelCorr[i]=0.0;
modelCorr_new=new double [thisCorrelationSize*thisCorrelationSize];
for (int i=0;i<modelCorr.length; i++) modelCorr[i]=0.0;
for (int i=0;i<modelCorr_new.length;i++) modelCorr_new[i]=0.0;
for (int dy=0;dy<2;dy++) for (int dx=0;dx<2;dx++) {
for (int y=0;y<halfSize;y++) for (int x=0;x<halfSize;x++) {
modelCorr[(2*y+dy)*thisCorrelationSize+(2*x+dx)]+=
modelCorrs[2*dy+dx][(qSize+y)*thisCorrelationSize+(qSize+x)];
modelCorr_new[(2*y+dy)*thisCorrelationSize+(2*x+dx)]+=
modelCorrs_new[2*dy+dx][(qSize+y)*thisCorrelationSize+(qSize+x)];
}
}
thisLowpass/=2.0; // the lower the value, the more filtering. Decimated twice,so low pass filtering - accordingly
thisFFTSubdiv=(thisFFTSubdiv>1)?(thisFFTSubdiv/2):1;
} else {
modelCorr=modelCorrs[0]; // also - different size
modelCorr= modelCorrs[0]; // also - different size
modelCorr_new=modelCorrs_new[0]; // also - different size
}
if (debug_level > (debug_threshold + 0)){
System.out.println(">==========Showing modelCorr");
SDFA_INSTANCE.showArrays(modelCorr, thisCorrelationSize,thisCorrelationSize, "modelCorr");
}
double [] centerXY_new;
if (fast) centerXY_new= correlationMaximum( // maybe twice actual size if
modelCorr_new,
distortionParameters.correlationMaxOffset,
(debug_level > (debug_threshold + 0)) && (numNeib==0)); // low-pass filtering should already be done
else centerXY_new= correlationMaximum(
modelCorr_new,
distortionParameters.correlationRadius,
distortionParameters.correlationThreshold, //double threshold, // fraction of maximum (slightly less than 1.0) to limit the top part of the maximum for centroid
distortionParameters.correlationSubdiv,
thisFFTSubdiv,
fht_instance,
distortionParameters.correlationMaxOffset,
thisLowpass, //distortionParameters.correlationLowPassSigma
// (debug_level>2) && (passNumber>1));
(debug_level > (debug_threshold + 0)));
if (fast) centerXY= correlationMaximum( // maybe twice actual size if
modelCorr,
distortionParameters.correlationMaxOffset,
(debug_level > (debug_threshold + 0)) && (numNeib==0)); // low-pass filtering should already be done
else centerXY= correlationMaximum(modelCorr,
else centerXY= correlationMaximum(
modelCorr,
distortionParameters.correlationRadius,
distortionParameters.correlationThreshold, //double threshold, // fraction of maximum (slightly less than 1.0) to limit the top part of the maximum for centroid
......@@ -9397,38 +9564,33 @@ dbgThis=true;
if (numNeib>1){
centerXY[0]*=0.5;
centerXY[1]*=0.5;
centerXY_new[0]*=0.5;
centerXY_new[1]*=0.5;
for (int i=0;i<2;i++) for (int j=0;j<2;j++) WVgreens[i][j]*=0.5;
}
/*
contrast= correlationContrast1(
modelCorr,
WVgreens, // wave vectors (same units as the pixels array)
distortionParameters.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
//TODO: verify that displacement is correct here (sign, direction)
centerXY[0], // x0, // center coordinates
centerXY[1], //y0,
"test-contrast", // title base for optional plots names
debug_level);
result[2]=contrast;
if ((distortionParameters.correlationMinContrast>0) && (contrast<distortionParameters.correlationMinContrast)) {
// if (debug_level>1) System.out.println("Contrast too low - "+contrast+"<"+distortionParameters.correlationMinContrast);
if (debug_level>1) System.out.println("Contrast "+IJ.d2s(contrast,3)+" ("+distortionParameters.correlationMinContrast+")"+
" is too low ( probed around "+IJ.d2s(beforeXY[0],3)+"/"+IJ.d2s(beforeXY[1],3)+")->"+
IJ.d2s(centerXY[0],3)+"/"+IJ.d2s(centerXY[1],3));
return null;
}
*/
double [] contrasts_new= correlationContrast(
modelCorr_new,
greens,
WVgreens, // wave vectors (same units as the pixels array)
distortionParameters.contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (pixels, 2.0)
distortionParameters.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
centerXY[0], // x0, // center coordinates
centerXY[1], //y0,
"test-contrast-new"); // title base for optional plots names
double [] contrasts= correlationContrast(
modelCorr,
greens,
WVgreens, // wave vectors (same units as the pixels array)
distortionParameters.contrastSelectSigmaCenter, // Gaussian sigma to select correlation (pixels, 2.0)
distortionParameters.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
distortionParameters.contrastAverageSigma,
centerXY[0], // x0, // center coordinates
centerXY[1], //y0,
"test-contrast"); // title base for optional plots names
if ((debug_level > (debug_threshold - 1))) {
System.out.println("contrast_new = "+contrasts_new[0]+", contrast = "+contrasts[0]);
}
contrast=contrasts[0];
result[2]=contrast;
if (Double.isNaN(contrasts[0]) || ((distortionParameters.correlationMinContrast>0) && (contrasts[0]<distortionParameters.correlationMinContrast))) {
......@@ -9477,14 +9639,6 @@ dbgThis=true;
}
/* ======= Debugging only - returns 2-d array of x,y as a function of initial estimation =================== */
public double [][][] scanPatternCrossLocation(
double range, // size of the scanning square
......@@ -10941,6 +11095,7 @@ error=Sum(W(x,y)*(F^2 + 2*F*(A*x^2+B*y^2+C*x*y+D*x+E*y-Z(x,y)) +(...) )
public double correlationMinAbsoluteInitialContrast; // minimal contrast for the pattern of the center (initial point)
public double scaleFirstPassContrast; // Decrease contrast of cells that are too close to the border to be processed in refinement pass
public double contrastSelectSigmaCenter; // Gaussian sigma to select correlation centers in pixels, 2.0 (center spot)
public double contrastSelectSigma; // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
public double contrastAverageSigma; // Gaussian sigma to average correlation variations (as contrast reference) 0.5
......@@ -11010,6 +11165,7 @@ error=Sum(W(x,y)*(F^2 + 2*F*(A*x^2+B*y^2+C*x*y+D*x+E*y-Z(x,y)) +(...) )
double correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point)
double scaleFirstPassContrast, // Decrease contrast of cells that are too close to the border to be processed in refinement pass
double contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (fraction of UV period), 0.02 (center spot)
double contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
double contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5
int minimalPatternCluster, // minimal pattern cluster size (0 - disable retries)
......@@ -11071,6 +11227,7 @@ error=Sum(W(x,y)*(F^2 + 2*F*(A*x^2+B*y^2+C*x*y+D*x+E*y-Z(x,y)) +(...) )
this.correlationMinAbsoluteContrast=correlationMinAbsoluteContrast; // minimal contrast for the pattern to pass, does not compensate for low ligt
this.correlationMinAbsoluteInitialContrast=correlationMinAbsoluteInitialContrast; // minimal contrast for the pattern of the center (initial point)
this.scaleFirstPassContrast=scaleFirstPassContrast; // Decrease contrast of cells that are too close to the border to be processed in refinement pass
this.contrastSelectSigmaCenter = contrastSelectSigmaCenter; // Gaussian sigma to select correlation centers (pixels, 2.0)
this.contrastSelectSigma=contrastSelectSigma; // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
this.contrastAverageSigma=contrastAverageSigma; // Gaussian sigma to average correlation variations (as contrast reference) 0.5
this.minimalPatternCluster=minimalPatternCluster; // minimal pattern cluster size (0 - disable retries)
......@@ -11135,6 +11292,7 @@ error=Sum(W(x,y)*(F^2 + 2*F*(A*x^2+B*y^2+C*x*y+D*x+E*y-Z(x,y)) +(...) )
this.correlationMinAbsoluteContrast, // minimal contrast for the pattern to pass, does not compensate for low ligt
this.correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point)
this.scaleFirstPassContrast, // Decrease contrast of cells that are too close to the border to be processed in refinement pass
this.contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (pixels, 2.0)
this.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
this.contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5
this.minimalPatternCluster, // minimal pattern cluster size (0 - disable retries)
......@@ -11198,6 +11356,7 @@ error=Sum(W(x,y)*(F^2 + 2*F*(A*x^2+B*y^2+C*x*y+D*x+E*y-Z(x,y)) +(...) )
properties.setProperty(prefix+"correlationMinAbsoluteContrast",this.correlationMinAbsoluteContrast+"");
properties.setProperty(prefix+"correlationMinAbsoluteInitialContrast",this.correlationMinAbsoluteInitialContrast+"");
properties.setProperty(prefix+"scaleFirstPassContrast",this.scaleFirstPassContrast+"");
properties.setProperty(prefix+"contrastSelectSigmaCenter",this.contrastSelectSigmaCenter+"");
properties.setProperty(prefix+"contrastSelectSigma",this.contrastSelectSigma+"");
properties.setProperty(prefix+"contrastAverageSigma",this.contrastAverageSigma+"");
properties.setProperty(prefix+"minimalPatternCluster",this.minimalPatternCluster+"");
......@@ -11280,6 +11439,8 @@ error=Sum(W(x,y)*(F^2 + 2*F*(A*x^2+B*y^2+C*x*y+D*x+E*y-Z(x,y)) +(...) )
if (properties.getProperty(prefix+"scaleFirstPassContrast")!=null)
this.scaleFirstPassContrast=Double.parseDouble(properties.getProperty(prefix+"scaleFirstPassContrast"));
if (properties.getProperty(prefix+"contrastSelectSigmaCenter")!=null)
this.contrastSelectSigmaCenter=Double.parseDouble(properties.getProperty(prefix+"contrastSelectSigmaCenter"));
if (properties.getProperty(prefix+"contrastSelectSigma")!=null)
this.contrastSelectSigma=Double.parseDouble(properties.getProperty(prefix+"contrastSelectSigma"));
if (properties.getProperty(prefix+"contrastAverageSigma")!=null)
......
src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java
View file @ 9f0c8d98
......@@ -1358,7 +1358,11 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
itr=set.iterator();
while(itr.hasNext()) {
str = (String) itr.next();
imp_dst.setProperty(str,prop.getProperty(str));
try {
imp_dst.setProperty(str,prop.getProperty(str));
} catch (Exception e) {
imp_dst.setProperty(str,"");
}
}
}
}
......
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