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imagej-elphel
Commit e1398902 authored by Andrey Filippov's avatar Andrey Filippov
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committing w/o breaking - 8

parent 908623d9
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src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java
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...@@ -2327,9 +2327,14 @@ public class EyesisAberrations { ...@@ -2327,9 +2327,14 @@ public class EyesisAberrations {
if (PSFBooleanMap[nTileY][nTileX]) { if (PSFBooleanMap[nTileY][nTileX]) {
tilesToProcessXY[ncell ][0]=nTileX; tilesToProcessXY[ncell ][0]=nTileX;
tilesToProcessXY[ncell ][1]=nTileY; tilesToProcessXY[ncell ][1]=nTileY;
tilesToProcessXY[ncell ][2]=(sampleList==null)?(fft_overlap*2*nTileX):sampleList[nTileY][nTileX][0]; tilesToProcessXY[ncell ][2]=(sampleList==null)?(tile_overlap * nTileX) : sampleList[nTileY][nTileX][0];
tilesToProcessXY[ncell++][3]=(sampleList==null)?(fft_overlap*2*nTileY):sampleList[nTileY][nTileX][1]; tilesToProcessXY[ncell++][3]=(sampleList==null)?(tile_overlap * nTileY) : sampleList[nTileY][nTileX][1];
if (is_mono) {
pdfKernelMap[nTileY][nTileX]=new double[1][];
} else {
pdfKernelMap[nTileY][nTileX]=new double[colorComponents.colorsToCorrect.length][]; pdfKernelMap[nTileY][nTileX]=new double[colorComponents.colorsToCorrect.length][];
}
} else pdfKernelMap[nTileY][nTileX]=null; } else pdfKernelMap[nTileY][nTileX]=null;
} }
final double [][][][] debugLateral=new double [PSFBooleanMap.length][PSFBooleanMap[0].length][][]; final double [][][][] debugLateral=new double [PSFBooleanMap.length][PSFBooleanMap[0].length][][];
...@@ -2385,13 +2390,13 @@ public class EyesisAberrations { ...@@ -2385,13 +2390,13 @@ public class EyesisAberrations {
if (updateStatus) IJ.showStatus("Processing tile["+nTY+"]["+nTX+"] ("+(nTile+1)+" of "+patternCells+")"); if (updateStatus) IJ.showStatus("Processing tile["+nTY+"]["+nTX+"] ("+(nTile+1)+" of "+patternCells+")");
if (masterDebugLevel>1) System.out.println("#!# "+x0+":"+y0+" Processing tile["+nTY+"]["+nTX+"] ("+(nTile+1)+" of "+patternCells+") : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)); if (masterDebugLevel>1) System.out.println("#!# "+x0+":"+y0+" Processing tile["+nTY+"]["+nTX+"] ("+(nTile+1)+" of "+patternCells+") : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (overexposed!=null){ if (overexposed!=null){
over=JP4_INSTANCE.fracOverExposed(overexposed, // map of overexposed pixels 0.0 - 0K, >0 (==1.0) - overexposed over=JP4_INSTANCE.fracOverExposed(
overexposed, // map of overexposed pixels 0.0 - 0K, >0 (==1.0) - overexposed
mapWidth, // width of the map mapWidth, // width of the map
x0, // X of the top left corner of the selection x0, // X of the top left corner of the selection
y0, // Y of the top left corner of the selection y0, // Y of the top left corner of the selection
2*fft_size, // selection width tile_size, // selection width
2*fft_size); // selection height tile_size); // selection height
// if ((globalDebugLevel>0) && (over>0.0)) System.out.println("Overexposed fraction of "+over+" at x0="+x0+" y0="+y0+" width"+(2*fft_size));
} else over=-1.0; } else over=-1.0;
if ( over > overexposedAllowed) { if ( over > overexposedAllowed) {
pdfKernelMap[nTY][nTX]=null; pdfKernelMap[nTY][nTX]=null;
...@@ -2402,7 +2407,7 @@ public class EyesisAberrations { ...@@ -2402,7 +2407,7 @@ public class EyesisAberrations {
} }
kernels=getPSFKernels(imp_sel, kernels=getPSFKernels(imp_sel,
simArray, //simulation image, scaled PSF_subpixel/2 simArray, //simulation image, scaled PSF_subpixel/2
2*fft_size, // size in pixels (twice fft_size) tile_size, // 2*fft_size, // size in pixels (twice fft_size for Bayer only?)
x0, // top left corner X (pixels) x0, // top left corner X (pixels)
y0, // top left corner Y (pixels) y0, // top left corner Y (pixels)
simulationPattern, simulationPattern,
...@@ -2672,7 +2677,7 @@ public class EyesisAberrations { ...@@ -2672,7 +2677,7 @@ public class EyesisAberrations {
public double [][] getPSFKernels ( ImagePlus imp, 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) 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 tile_size, // size in pixels (twice FFT_SIZE for Bayer, equals FFT size for mono)
int x0, // top left corner X (pixels) int x0, // top left corner X (pixels)
int y0, // top left corner Y (pixels) int y0, // top left corner Y (pixels)
SimulationPattern simulationPattern, SimulationPattern simulationPattern,
...@@ -2717,7 +2722,8 @@ public class EyesisAberrations { ...@@ -2717,7 +2722,8 @@ public class EyesisAberrations {
if ((simArray==null) || (psfParameters.approximateGrid)){ // just for testing(never here?) if ((simArray==null) || (psfParameters.approximateGrid)){ // just for testing(never here?)
/* Calculate pattern parameters, including distortion */ /* Calculate pattern parameters, including distortion */
if (matchSimulatedPattern.PATTERN_GRID==null) { if (matchSimulatedPattern.PATTERN_GRID==null) {
double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(input_bayer_or_mono, // pixel array to process (no windowing!) double[][] distortedPattern= matchSimulatedPattern.findPatternDistorted(
input_bayer_or_mono, // pixel array to process (no windowing!)
patternDetectParameters, patternDetectParameters,
patternDetectParameters.minGridPeriod/2, patternDetectParameters.minGridPeriod/2,
patternDetectParameters.maxGridPeriod/2, patternDetectParameters.maxGridPeriod/2,
...@@ -2826,7 +2832,7 @@ public class EyesisAberrations { ...@@ -2826,7 +2832,7 @@ public class EyesisAberrations {
System.out.println ("Error, No UV pattern @ x="+(PSFCell.x+PSFCell.width/2)+", y="+(PSFCell.y+PSFCell.height/2)); System.out.println ("Error, No UV pattern @ x="+(PSFCell.x+PSFCell.width/2)+", y="+(PSFCell.y+PSFCell.height/2));
return null; return null;
} }
// int [] iUV={index % matchSimulatedPattern.getDArrayHeight(), index / matchSimulatedPattern.getDArrayHeight()}; // TODO: make sure it is correct?
int [] iUV={index % matchSimulatedPattern.getDArrayWidth(), index / matchSimulatedPattern.getDArrayWidth()}; // TODO: make sure it is correct? int [] iUV={index % matchSimulatedPattern.getDArrayWidth(), index / matchSimulatedPattern.getDArrayWidth()}; // TODO: make sure it is correct?
if (matchSimulatedPattern.getDArray(iUV[1],iUV[0])==null) { if (matchSimulatedPattern.getDArray(iUV[1],iUV[0])==null) {
if (globalDebugLevel>0){ if (globalDebugLevel>0){
...@@ -2837,18 +2843,21 @@ public class EyesisAberrations { ...@@ -2837,18 +2843,21 @@ public class EyesisAberrations {
} }
return null; return null;
} }
if (matchSimulatedPattern.getDArray(iUV[1],iUV[0],1)==null) { if (matchSimulatedPattern.getDArray(iUV[1],iUV[0],1)==null) {
if (globalDebugLevel>0) System.out.println ( "Tried to extract non-existent wave vectors from "+iUV[0]+"/"+iUV[1]); if (globalDebugLevel>0) System.out.println ( "Tried to extract non-existent wave vectors from "+iUV[0]+"/"+iUV[1]);
return null; return null;
} }
//TODO: Need to define wave vectors here - how? //TODO: Need to define wave vectors here - how?
wVectors[0]=matchSimulatedPattern.getDArray(iUV[1],iUV[0],1); //null pointer wVectors[0]=matchSimulatedPattern.getDArray(iUV[1],iUV[0],1); //null pointer
wVectors[1]=matchSimulatedPattern.getDArray(iUV[1],iUV[0],2); wVectors[1]=matchSimulatedPattern.getDArray(iUV[1],iUV[0],2);
// should it be averaged WV? // should it be averaged WV?
if (globalDebugLevel>2) System.out.println ( " x0="+x0+" y0="+y0); if (globalDebugLevel>2) System.out.println ( " x0="+x0+" y0="+y0);
if (globalDebugLevel>2) SDFA_INSTANCE.showArrays(input_bayer_or_mono, 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) SDFA_INSTANCE.showArrays(simul_pixels, true, title+"-S");
//if (globalDebugLevel>2) System.out.println (simArray[0][-1]); // cause error
if (masterDebugLevel>1){ if (masterDebugLevel>1){
dbgSimPix=new double[simul_pixels.length][]; dbgSimPix=new double[simul_pixels.length][];
for (int ii=0;ii<dbgSimPix.length;ii++) for (int ii=0;ii<dbgSimPix.length;ii++)
...@@ -2866,17 +2875,21 @@ public class EyesisAberrations { ...@@ -2866,17 +2875,21 @@ public class EyesisAberrations {
subpixel); // same as used in oversampleFFTInput() - oversampling ratio subpixel); // same as used in oversampleFFTInput() - oversampling ratio
} }
for (i=0;i<4;i++) if (!colorComponents.colorsToCorrect[i]) input_bayer_or_mono[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) { if (debugThis) {
// SDFA_INSTANCE.showArrays(input_bayer, fft_size*subpixel, fft_size*subpixel, title); // SDFA_INSTANCE.showArrays(input_bayer, fft_size*subpixel, fft_size*subpixel, title);
} }
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); 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)){ 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 (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_or_mono, 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 (debugThis) SDFA_INSTANCE.showArrays(simul_pixels, true, title+"-SIM");
//if (globalDebugLevel>2)globalDebugLevel=0; //************************************************************ //if (globalDebugLevel>2)globalDebugLevel=0; //************************************************************
double [][] inverted=new double[colorComponents.colorsToCorrect.length][]; double [][] inverted=new double[colorComponents.colorsToCorrect.length][];
double wvAverage=Math.sqrt(0.5*(wVectors[0][0]*wVectors[0][0]+wVectors[0][1]*wVectors[0][1]+ 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])); wVectors[1][0]*wVectors[1][0]+wVectors[1][1]*wVectors[1][1]));
...@@ -2884,7 +2897,8 @@ public class EyesisAberrations { ...@@ -2884,7 +2897,8 @@ public class EyesisAberrations {
for (i=0;(i<input_bayer_or_mono.length) && (i<simul_pixels.length);i++) if ((colorComponents.colorsToCorrect[i]) && (input_bayer_or_mono[i]!=null)){ 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 ( "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); 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], inverted[i]=limitedInverseOfFHT(
input_bayer_or_mono[i],
simul_pixels[i], simul_pixels[i],
fft_size*subpixel, fft_size*subpixel,
(i==5), // boolean checker // checkerboard pattern in the source file (use when filtering) (i==5), // boolean checker // checkerboard pattern in the source file (use when filtering)
......
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