Commit e1398902 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

committing w/o breaking - 8

parent 908623d9

src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java

+26 −12
Original line number Diff line number Diff line
@@ -2327,9 +2327,14 @@ public class EyesisAberrations { 
			if (PSFBooleanMap[nTileY][nTileX]) {

				tilesToProcessXY[ncell  ][0]=nTileX;

				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];

				tilesToProcessXY[ncell  ][2]=(sampleList==null)?(tile_overlap * nTileX) : sampleList[nTileY][nTileX][0];

				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][];

				}



			} else pdfKernelMap[nTileY][nTileX]=null;

		}

		final double [][][][] debugLateral=new double [PSFBooleanMap.length][PSFBooleanMap[0].length][][];
@@ -2385,13 +2390,13 @@ public class EyesisAberrations { 
						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 (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

									x0,          // X of the top left corner of the selection

									y0,          // Y of the top left corner of the selection

									2*fft_size,  // selection width

									2*fft_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));

									tile_size,   // selection width

									tile_size);  // selection height

						} else over=-1.0;

						if ( over > overexposedAllowed) {

							pdfKernelMap[nTY][nTX]=null;
@@ -2402,7 +2407,7 @@ public class EyesisAberrations { 
							}

							kernels=getPSFKernels(imp_sel,

									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)

									y0,               // top left corner Y (pixels)

									simulationPattern,
@@ -2672,7 +2677,7 @@ 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 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                   y0,          // top left corner Y (pixels)

			SimulationPattern     simulationPattern,
@@ -2717,7 +2722,8 @@ 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_or_mono, // 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,
@@ -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));

				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?

			if (matchSimulatedPattern.getDArray(iUV[1],iUV[0])==null) {

				if (globalDebugLevel>0){
@@ -2837,18 +2843,21 @@ public class EyesisAberrations { 
				}

				return 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]);

				return null;

			}



			//TODO:  Need to define wave vectors here - how?

			wVectors[0]=matchSimulatedPattern.getDArray(iUV[1],iUV[0],1); //null pointer

			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_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){

				dbgSimPix=new double[simul_pixels.length][];

				for (int ii=0;ii<dbgSimPix.length;ii++)
@@ -2866,17 +2875,21 @@ public class EyesisAberrations { 
					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



		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_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_or_mono, true, title+"-input");

		if (debugThis) SDFA_INSTANCE.showArrays(simul_pixels, true, title+"-SIM");



//if (globalDebugLevel>2)globalDebugLevel=0; //************************************************************



		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]+

				wVectors[1][0]*wVectors[1][0]+wVectors[1][1]*wVectors[1][1]));
@@ -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)){

				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],

				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)