Added absoulte center option, debugging missing of the grid (7d08fe37) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+12 −4

src/main/java/Distortions.java

+2 −1

Original line number	Original line	Diff line number	Diff line
	@@ -3060,8 +3060,9 @@ For each point in the image
	cell[0], //double px,		cell[0], //double px,
	cell[1]); //double py)		cell[1]); //double py)
	cell[0]+=corrXYARGB[0]; // measured-> corrected : subtract, projected->simulated:add;		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;		return true;
	}		}

src/main/java/EyesisAberrations.java

+30 −20

Original line number	Original line	Diff line number	Diff line
	@@ -1446,7 +1446,7 @@ public class EyesisAberrations {
	int globalDebugLevel		int globalDebugLevel
	){		){
	double [][][][] psfKernelMap; // will be lost - do we need it outside		double [][][][] psfKernelMap; // will be lost - do we need it outside
	double [][][][][] kernelsElllipsePars = new double[filenames.length][][][][];		double [][][][][] kernelsElllipsePars = new double[filenames.length][][][][]; //x0,y0,a,b,c,area
	if (thisDebugLevel>0){		if (thisDebugLevel>0){
	System.out.println("combinePSFKernels(): filenames.length="+filenames.length);		System.out.println("combinePSFKernels(): filenames.length="+filenames.length);
	}		}
	@@ -1503,15 +1503,15 @@ public class EyesisAberrations {
	// System.out.println("nChn="+nChn+" nFile="+nFile+" tileY="+tileY+" tileX="+tileX);		// System.out.println("nChn="+nChn+" nFile="+nFile+" tileY="+tileY+" tileX="+tileX);
	if (kernelsElllipsePars[nFile][tileY][tileX][chn]!=null) {		if (kernelsElllipsePars[nFile][tileY][tileX][chn]!=null) {
	channels[chn]=true;		channels[chn]=true;
	c[0][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][0];		c[0][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][0]; // x0
	c[1][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][1];		c[1][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][1]; // y0
	c[2][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][2];		c[2][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][2]; // a
	c[3][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][3];		c[3][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][3]; // b
	c[4][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][4];		c[4][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][4]; // c
	a=1/Math.sqrt(kernelsElllipsePars[nFile][tileY][tileX][chn][2]*kernelsElllipsePars[nFile][tileY][tileX][chn][3]-		a=1/Math.sqrt(kernelsElllipsePars[nFile][tileY][tileX][chn][2]*kernelsElllipsePars[nFile][tileY][tileX][chn][3]-
	kernelsElllipsePars[nFile][tileY][tileX][chn][4]*kernelsElllipsePars[nFile][tileY][tileX][chn][4]/4);		kernelsElllipsePars[nFile][tileY][tileX][chn][4]*kernelsElllipsePars[nFile][tileY][tileX][chn][4]/4);
	c[5][chn][nFile+1][tileY*kWidth+tileX]= Math.sqrt(a); // radius		c[5][chn][nFile+1][tileY*kWidth+tileX]= Math.sqrt(a); // radius
	c[6][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][5];		c[6][chn][nFile+1][tileY*kWidth+tileX]=kernelsElllipsePars[nFile][tileY][tileX][chn][5]; // area

	} else {		} else {
	c[0][chn][nFile+1][tileY*kWidth+tileX]=Double.NaN;		c[0][chn][nFile+1][tileY*kWidth+tileX]=Double.NaN;
	@@ -2057,7 +2057,8 @@ public class EyesisAberrations {
	"",		"",
	debugLevel);		debugLevel);
	// ellipseCoeffs[tileY][tileX][chn]=findEllipseOnPSF(kernel, selection, "");		// ellipseCoeffs[tileY][tileX][chn]=findEllipseOnPSF(kernel, selection, "");
	ec=findEllipseOnPSF(kernel, selection, "", debugLevel);		ec=findEllipseOnPSF(kernel, selection, "", debugLevel); // x0,y0,a,b,c (r2= a* x^2+by^2+cxy)

	l=ec.length;		l=ec.length;
	ellipseCoeffs[tileY][tileX][chn]=new double[l+1];		ellipseCoeffs[tileY][tileX][chn]=new double[l+1];
	for (i=0;i<ec.length;i++) ellipseCoeffs[tileY][tileX][chn][i]=ec[i];		for (i=0;i<ec.length;i++) ellipseCoeffs[tileY][tileX][chn][i]=ec[i];
	@@ -2776,6 +2777,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	globalDebugLevel,		globalDebugLevel,
	title+"-"+i);		title+"-"+i);
	}		}
			int debugThreshold=1;
	if (debugThis) SDFA_INSTANCE.showArrays(inverted, fft_sizesubpixel, fft_sizesubpixel, title+"_Combined-PSF");		if (debugThis) SDFA_INSTANCE.showArrays(inverted, fft_sizesubpixel, fft_sizesubpixel, title+"_Combined-PSF");
	/* correct composite greens */		/* correct composite greens */
	/* Here we divide wave vectors by subpixel as the pixels are already added */		/* Here we divide wave vectors by subpixel as the pixels are already added */
	@@ -2811,7 +2813,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	//int [][] clusterMask;		//int [][] clusterMask;
	/* Start with referenceComp */		/* Start with referenceComp */
	i= referenceComp;		i= referenceComp;
	if (globalDebugLevel>2) {		if (globalDebugLevel>debugThreshold) {
	System.out.println(x0+":"+y0+"1-PSF_shifts.length= "+PSF_shifts.length+" i="+i+" input_bayer.length="+input_bayer.length);		System.out.println(x0+":"+y0+"1-PSF_shifts.length= "+PSF_shifts.length+" i="+i+" input_bayer.length="+input_bayer.length);
	System.out.println("Before: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+		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));		" PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3));
	@@ -2819,7 +2821,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************


	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)
	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_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		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)		(i==4)?wVectors4:wVectors, // two wave vectors, lengths in cycles/pixel (pixels match pixel array)
	@@ -2829,13 +2831,13 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	(globalDebugLevel>4),		(globalDebugLevel>4),
	globalDebugLevel		globalDebugLevel
	);		);
	if (globalDebugLevel>2) 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_shifts["+i+"][0]="+IJ.d2s(PSF_shifts [i][0],3)+" PSF_shifts["+i+"][1]="+IJ.d2s( PSF_shifts[i][1],3));
	if (globalDebugLevel>2) 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 (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) { /* 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)) {		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);		PSF_shifts[j]=shiftSensorToBayer (shiftBayerToSensor(PSF_shifts[referenceComp],referenceComp,subpixel),j,subpixel);
	if (globalDebugLevel>2) 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));		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));
	}		}
	}		}

	@@ -2846,7 +2848,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	lateralChromaticAbs[i]=Math.sqrt(lateralChromatic[i][0]lateralChromatic[i][0]+lateralChromatic[i][1]lateralChromatic[i][1]);		lateralChromaticAbs[i]=Math.sqrt(lateralChromatic[i][0]lateralChromatic[i][0]+lateralChromatic[i][1]lateralChromatic[i][1]);
	/* Now process all the other components */		/* 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.length;i++) if ((i!=referenceComp) && (colorComponents.colorsToCorrect[i])) {
	if (globalDebugLevel>2) {		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.length);

	System.out.println(x0+":"+y0+"Before: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+		System.out.println(x0+":"+y0+"Before: color Component "+i+" PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+
	@@ -2862,8 +2864,8 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	title+"_"+i, // reduce the PSF cell size to this part of the area connecting first negative clones		title+"_"+i, // reduce the PSF cell size to this part of the area connecting first negative clones
	(globalDebugLevel>4),		(globalDebugLevel>4),
	globalDebugLevel);		globalDebugLevel);
	if (globalDebugLevel>2) 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_shifts["+i+"][0]="+IJ.d2s(PSF_shifts [i][0],3)+" PSF_shifts["+i+"][1]="+IJ.d2s( PSF_shifts[i][1],3));
	if (globalDebugLevel>2) 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 (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));
	lateralChromatic[i]=shiftBayerToSensor ( PSF_shifts[i][0]+PSF_centroids[i][0],		lateralChromatic[i]=shiftBayerToSensor ( PSF_shifts[i][0]+PSF_centroids[i][0],
	PSF_shifts[i][1]+PSF_centroids[i][1],		PSF_shifts[i][1]+PSF_centroids[i][1],
	i,		i,
	@@ -2873,9 +2875,10 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	}		}
	if (globalDebugLevel>1) { //1		if (globalDebugLevel>1) { //1
	for (i=0;i<PSF_shifts.length;i++) if (colorComponents.colorsToCorrect[i]){		for (i=0;i<PSF_shifts.length;i++) if (colorComponents.colorsToCorrect[i]){
	if (globalDebugLevel>2) { //2		if (globalDebugLevel>debugThreshold) { //2
	System.out.println(x0+":"+y0+" Color Component "+i+" subpixel="+subpixel+		System.out.println(x0+":"+y0+" Color Component "+i+" subpixel="+subpixel+
	" psfParameters.ignoreChromatic="+psfParameters.ignoreChromatic+		" psfParameters.ignoreChromatic="+psfParameters.ignoreChromatic+
			" psfParameters.absoluteCenter="+psfParameters.absoluteCenter+
	" psfParameters.symm180="+psfParameters.symm180);		" psfParameters.symm180="+psfParameters.symm180);
	System.out.println(x0+":"+y0+ " PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+		System.out.println(x0+":"+y0+ " PSF_shifts["+i+"][0]="+IJ.d2s(PSF_shifts[i][0],3)+
	" PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3)+		" PSF_shifts["+i+"][1]="+IJ.d2s(PSF_shifts[i][1],3)+
	@@ -3339,7 +3342,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	debugLevel);		debugLevel);
	// true);		// 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);		// 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])}		// TODO: Shift +/- 0.5 Pix here {centerXY[0]-Math.round(centerXY[0]),centerXY[1]-Math.round(centerXY[1])}
	@@ -3397,7 +3400,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	if (debugLevel>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));		if (debugLevel>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) */		/* 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) {		if (centerXY!=null) {
	centerXY[0]+=centroidXY[0];		centerXY[0]+=centroidXY[0];
	centerXY[1]+=centroidXY[1];		centerXY[1]+=centroidXY[1];
	@@ -4908,6 +4911,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	public boolean useWindow;		public boolean useWindow;
	public boolean symm180;		public boolean symm180;
	public boolean ignoreChromatic;		public boolean ignoreChromatic;
			public boolean absoluteCenter;
	public double smoothSeparate;		public double smoothSeparate;
	public double topCenter;		public double topCenter;
	public double sigmaToRadius;		public double sigmaToRadius;
	@@ -4927,6 +4931,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	boolean useWindow,		boolean useWindow,
	boolean symm180,		boolean symm180,
	boolean ignoreChromatic,		boolean ignoreChromatic,
			boolean absoluteCenter,
	double smoothSeparate,		double smoothSeparate,
	double topCenter,		double topCenter,
	double sigmaToRadius,		double sigmaToRadius,
	@@ -4946,6 +4951,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	this.useWindow = useWindow;		this.useWindow = useWindow;
	this.symm180 = symm180;		this.symm180 = symm180;
	this.ignoreChromatic = ignoreChromatic;		this.ignoreChromatic = ignoreChromatic;
			this.absoluteCenter=absoluteCenter;
	this.smoothSeparate = smoothSeparate;		this.smoothSeparate = smoothSeparate;
	this.topCenter = topCenter;		this.topCenter = topCenter;
	this.sigmaToRadius = sigmaToRadius;		this.sigmaToRadius = sigmaToRadius;
	@@ -4968,6 +4974,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	this.useWindow,		this.useWindow,
	this.symm180,		this.symm180,
	this.ignoreChromatic,		this.ignoreChromatic,
			this.absoluteCenter,
	this.smoothSeparate,		this.smoothSeparate,
	this.topCenter,		this.topCenter,
	this.sigmaToRadius,		this.sigmaToRadius,
	@@ -4988,6 +4995,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	properties.setProperty(prefix+"useWindow",this.useWindow+"");		properties.setProperty(prefix+"useWindow",this.useWindow+"");
	properties.setProperty(prefix+"symm180",this.symm180+"");		properties.setProperty(prefix+"symm180",this.symm180+"");
	properties.setProperty(prefix+"ignoreChromatic",this.ignoreChromatic+"");		properties.setProperty(prefix+"ignoreChromatic",this.ignoreChromatic+"");
			properties.setProperty(prefix+"absoluteCenter",this.absoluteCenter+"");
	properties.setProperty(prefix+"smoothSeparate",this.smoothSeparate+"");		properties.setProperty(prefix+"smoothSeparate",this.smoothSeparate+"");
	properties.setProperty(prefix+"topCenter",this.topCenter+"");		properties.setProperty(prefix+"topCenter",this.topCenter+"");
	properties.setProperty(prefix+"sigmaToRadius",this.sigmaToRadius+"");		properties.setProperty(prefix+"sigmaToRadius",this.sigmaToRadius+"");
	@@ -5007,6 +5015,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	properties.setProperty(prefix+"useWindow",this.useWindow+"");		properties.setProperty(prefix+"useWindow",this.useWindow+"");
	properties.setProperty(prefix+"symm180",this.symm180+"");		properties.setProperty(prefix+"symm180",this.symm180+"");
	properties.setProperty(prefix+"ignoreChromatic",this.ignoreChromatic+"");		properties.setProperty(prefix+"ignoreChromatic",this.ignoreChromatic+"");
			properties.setProperty(prefix+"absoluteCenter",this.absoluteCenter+"");
	properties.setProperty(prefix+"smoothSeparate",this.smoothSeparate+"");		properties.setProperty(prefix+"smoothSeparate",this.smoothSeparate+"");
	properties.setProperty(prefix+"topCenter",this.topCenter+"");		properties.setProperty(prefix+"topCenter",this.topCenter+"");
	properties.setProperty(prefix+"sigmaToRadius",this.sigmaToRadius+"");		properties.setProperty(prefix+"sigmaToRadius",this.sigmaToRadius+"");
	@@ -5027,6 +5036,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
	if (properties.getProperty(prefix+"useWindow")!=null) this.useWindow=Boolean.parseBoolean(properties.getProperty(prefix+"useWindow"));		if (properties.getProperty(prefix+"useWindow")!=null) this.useWindow=Boolean.parseBoolean(properties.getProperty(prefix+"useWindow"));
	if (properties.getProperty(prefix+"symm180")!=null) this.symm180=Boolean.parseBoolean(properties.getProperty(prefix+"symm180"));		if (properties.getProperty(prefix+"symm180")!=null) this.symm180=Boolean.parseBoolean(properties.getProperty(prefix+"symm180"));
	if (properties.getProperty(prefix+"ignoreChromatic")!=null) this.ignoreChromatic=Boolean.parseBoolean(properties.getProperty(prefix+"ignoreChromatic"));		if (properties.getProperty(prefix+"ignoreChromatic")!=null) this.ignoreChromatic=Boolean.parseBoolean(properties.getProperty(prefix+"ignoreChromatic"));
			if (properties.getProperty(prefix+"absoluteCenter")!=null) this.absoluteCenter=Boolean.parseBoolean(properties.getProperty(prefix+"absoluteCenter"));
	if (properties.getProperty(prefix+"smoothSeparate")!=null) this.smoothSeparate=Double.parseDouble(properties.getProperty(prefix+"smoothSeparate"));		if (properties.getProperty(prefix+"smoothSeparate")!=null) this.smoothSeparate=Double.parseDouble(properties.getProperty(prefix+"smoothSeparate"));
	if (properties.getProperty(prefix+"topCenter")!=null) this.topCenter=Double.parseDouble(properties.getProperty(prefix+"topCenter"));		if (properties.getProperty(prefix+"topCenter")!=null) this.topCenter=Double.parseDouble(properties.getProperty(prefix+"topCenter"));
	if (properties.getProperty(prefix+"sigmaToRadius")!=null) this.sigmaToRadius=Double.parseDouble(properties.getProperty(prefix+"sigmaToRadius"));		if (properties.getProperty(prefix+"sigmaToRadius")!=null) this.sigmaToRadius=Double.parseDouble(properties.getProperty(prefix+"sigmaToRadius"));

src/main/java/MatchSimulatedPattern.java

+6 −6

Original line number	Original line	Diff line number	Diff line
	@@ -3350,8 +3350,10 @@ public class MatchSimulatedPattern {
	if (!updating){		if (!updating){
	double [][] node=gn.getNode();		double [][] node=gn.getNode();
	double [] centerXY=node[0];		double [] centerXY=node[0];
	if (global_debug_level>1) {		if (global_debug_level>0) {
	System.out.println("distortions: node X/Y are "+centerXY[0]+"/"+centerXY[1]);		// 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 (debugLevel>1) {
	if (global_debug_level>1) {		if (global_debug_level>1) {
	@@ -3374,7 +3376,6 @@ public class MatchSimulatedPattern {
	if (global_debug_level>1) {		if (global_debug_level>1) {
	System.out.println("putInWaveList(waveFrontList, {"+centerUV[0]+","+centerUV[1]+"}, 0);");		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		// Each layer processing may be multi-threaded, they join before going to the next layer
	@@ -3453,7 +3454,7 @@ public class MatchSimulatedPattern {
	layer++;		layer++;
	if (updateStatus) IJ.showStatus("Correlating patterns, layer "+layer+(cleanup.get()?"(cleanup)":"")+", length "+waveFrontList.size());		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 (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		// starting layer
	cellNum.set(0);		cellNum.set(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	@@ -4077,11 +4078,10 @@ public class MatchSimulatedPattern {
	);		);
	if ((node!=null) && (node[0]!=null)) {		if ((node!=null) && (node[0]!=null)) {
	nodeQueue.add(new GridNode(node));		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		triedIndices[n]=true; // regardless - good or bad

	}		}
	}		}
	};		};

src/main/java/aberrations.java

+2 −0

Original line number	Original line	Diff line number	Diff line
	@@ -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		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 */		/* 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 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 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		public static double PSF_cutoff_energy=0.9; // Limit result kernel to proportional of the PSF, calculate initial cluster shape by this cutoff energy

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