Skip to content

I
imagej-elphel
Commit 7d08fe37 authored by Andrey Filippov's avatar Andrey Filippov
Browse files
Options

Added absoulte center option, debugging missing of the grid

parent 93c3e515
Expand all Hide whitespace changes
Inline Side-by-side
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
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, // 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
0.75, // 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
......@@ -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)
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_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)
......@@ -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_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)) {
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));
......@@ -17052,6 +17053,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //*********************************************
if (DEBUG_LEVEL>2) { //2
System.out.println("Color Component "+i+" subpixel="+subpixel+
" psfParameters.ignoreChromatic="+psfParameters.ignoreChromatic+
" psfParameters.absoluteCenter="+psfParameters.absoluteCenter+
" psfParameters.symm180="+psfParameters.symm180);
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)+
......@@ -17458,7 +17460,7 @@ if (DEBUG_LEVEL>2)DEBUG_LEVEL=0; //*********************************************
debug);
// 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);
// 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; //*********************************************
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) */
if (master || psfParameters.ignoreChromatic) {
if (!psfParameters.absoluteCenter && (master || psfParameters.ignoreChromatic)) {
if (centerXY!=null) {
centerXY[0]+=centroidXY[0];
centerXY[1]+=centroidXY[1];
......@@ -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 ("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 ("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: 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
......@@ -18958,6 +18963,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
psfParameters.useWindow= gd.getNextBoolean();
psfParameters.symm180= gd.getNextBoolean();
psfParameters.ignoreChromatic= gd.getNextBoolean();
psfParameters.absoluteCenter= gd.getNextBoolean();
psfParameters.smoothSeparate= gd.getNextNumber();
psfParameters.topCenter= gd.getNextNumber();
psfParameters.sigmaToRadius= gd.getNextNumber();
......@@ -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 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 ("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 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
psfParameters.wingsEnergy= gd.getNextNumber();
psfParameters.wingsEllipseScale= gd.getNextNumber();
psfParameters.ignoreChromatic= gd.getNextBoolean();
psfParameters.absoluteCenter= gd.getNextBoolean();
inverseParameters.otfCutoffEnergy= gd.getNextNumber();
inverseParameters.otfEllipseScale= gd.getNextNumber();
inverseParameters.otfEllipseGauss= gd.getNextBoolean();
......
src/main/java/Distortions.java
View file @ 7d08fe37
......@@ -3060,8 +3060,9 @@ For each point in the image
cell[0], //double px,
cell[1]); //double py)
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;
}
src/main/java/EyesisAberrations.java
View file @ 7d08fe37
This diff is collapsed.
src/main/java/MatchSimulatedPattern.java
View file @ 7d08fe37
......@@ -3350,8 +3350,10 @@ public class MatchSimulatedPattern {
if (!updating){
double [][] node=gn.getNode();
double [] centerXY=node[0];
if (global_debug_level>1) {
System.out.println("distortions: node X/Y are "+centerXY[0]+"/"+centerXY[1]);
if (global_debug_level>0) {
// 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 (global_debug_level>1) {
......@@ -3374,7 +3376,6 @@ public class MatchSimulatedPattern {
if (global_debug_level>1) {
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
......@@ -3453,7 +3454,7 @@ public class MatchSimulatedPattern {
layer++;
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 (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
cellNum.set(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
......@@ -4077,11 +4078,10 @@ public class MatchSimulatedPattern {
);
if ((node!=null) && (node[0]!=null)) {
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
}
}
};
......
src/main/java/aberrations.java
View file @ 7d08fe37
......@@ -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
/* 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 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
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment