debugging (d3b2b2c6) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+5 −0

src/main/java/MatchSimulatedPattern.java

+102 −3

Original line number	Original line	Diff line number	Diff line
	@@ -975,7 +975,7 @@ public class MatchSimulatedPattern {
	title, // title base for optional plots names		title, // title base for optional plots names
	this.debugLevel);		this.debugLevel);
	}		}
	public double correlationContrast ( double [] pixels, // square pixel array		public double correlationContrastOld ( double [] pixels, // square pixel array
	double [][] wVectors, // wave vectors (same units as the pixels array)		double [][] wVectors, // wave vectors (same units as the pixels array)
	double ringWidth, // ring (around r=0.5 dist to opposite corr) width		double ringWidth, // ring (around r=0.5 dist to opposite corr) width
	double x0, // center coordinates		double x0, // center coordinates
	@@ -1060,6 +1060,70 @@ public class MatchSimulatedPattern {
	}		}
	return contrast;		return contrast;
	}		}

			public double correlationContrast ( double [] pixels, // square pixel array
			double [][] wVectors, // wave vectors (same units as the pixels array)
			double ringWidth, // ring (around r=0.5 dist to opposite corr) width
			double x0, // center coordinates
			double y0,
			String title, // title base for optional plots names
			int debugLevel){
			double sigma=0.1;
			double sigma32=9sigmasigma;
			double k=-0.5/(sigma*sigma);
			double [][] sampleCentersXY={{0.0,0.0},{0.0,0.5},{0.5,0.0},{0.0,-0.5},{-0.5,0.0}};
			int [] sampleTypes = {0,1,1,1,1};
			int size=(int) Math.sqrt(pixels.length);
			double [] xy= new double [2];
			double [] uv;
			double r2;
			int i,j;
			/* opposite sign correlation points in uv are at uv=(0,-0.5),(0,0.5), (-0.5,0) and (0.5,0), with radius of (1/2)
			selecting center circle and a ring from 0.25 to 0.75 of the distance to opposite sign correlations */
			double [] dbgMask= new double[size*size];
			for (int n=0;n<dbgMask.length;n++) dbgMask[n]=0.0;
			double [] s={0.0,0.0};
			double [] w={0.0,0.0};
			for (i=0;i<size;i++) {
			xy[1]=i-size/2-y0;
			for (j=0;j<size;j++) {
			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=dxdx+dydy;
			if (r2<sigma32){
			double m=Math.exp(k*r2);
			dbgMask[i*size+j]+=m;
			w[sampleTypes[np]]+=m;
			s[sampleTypes[np]]+=mpixels[isize+j];
			}
			}
			}
			}
			if ((w[0]==0.0) \|\| (w[1]==0.0)) {
			if (debugLevel>1) System.out.println("Not enough data for correlation contrast: center - w[0]="+w[0]+" opposite - w[1]="+w[1]);
			return -1.0;
			}

			double contrast=Math.sqrt((s[0]/w[0])/(s[1]/w[1]));
			if (debugLevel>2) {
			System.out.println("Correlation contrast is "+contrast);
			double [][] dbgPixels={pixels,dbgMask};
			String [] titles={"all","mask"};
			(new showDoubleFloatArrays()).showArrays(
			dbgPixels,
			size,
			size,
			true,
			title+"_CORR_MASK",
			titles);
			}
			return contrast;
			}


	/* ======================================================================== */		/* ======================================================================== */
	public double[] correlateWithModel (double [] imagePixels, // measured pixel array		public double[] correlateWithModel (double [] imagePixels, // measured pixel array
	double [] modelPixels, // simulated (model) pixel array)		double [] modelPixels, // simulated (model) pixel array)
	@@ -7174,11 +7238,17 @@ y=xy0[1] + dUdeltaUV[0](xy1[1]-xy0[1])+dVdeltaUV[1](xy2[1]-xy0[1])
	double [] thisWindow=window;		double [] thisWindow=window;
	double uv_threshold=distortionParameters.minUVSpan0.25Math.sqrt(2.0);		double uv_threshold=distortionParameters.minUVSpan0.25Math.sqrt(2.0);

	if ((min_span<uv_threshold) && (window2!=null)) { // trying to increase only twice		if (
			(min_span<uv_threshold) &&
			(window2!=null) &&
			(thisCorrelationSize<distortionParameters.maximalCorrelationSize)) { // trying to increase only twice
	thisCorrelationSize*=2;		thisCorrelationSize*=2;
	min_span*=2;		min_span*=2;
	thisWindow=window2;		thisWindow=window2;
	if ((min_span<uv_threshold) && (window4!=null)) {		if (
			(min_span<uv_threshold) &&
			(window4!=null) &&
			(thisCorrelationSize<distortionParameters.maximalCorrelationSize)) {
	thisCorrelationSize*=2;		thisCorrelationSize*=2;
	min_span*=2;		min_span*=2;
	thisWindow=window4;		thisWindow=window4;
	@@ -7427,6 +7497,23 @@ y=xy0[1] + dUdeltaUV[0](xy1[1]-xy0[1])+dVdeltaUV[1](xy2[1]-xy0[1])
	double [] thisWindow=window;		double [] thisWindow=window;
	double uv_threshold=distortionParameters.minUVSpan0.25Math.sqrt(2.0);		double uv_threshold=distortionParameters.minUVSpan0.25Math.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;
			}
			}
			/*
	if ((min_span<uv_threshold) && (window2!=null)) { // trying to increase only twice		if ((min_span<uv_threshold) && (window2!=null)) { // trying to increase only twice
	thisCorrelationSize*=2;		thisCorrelationSize*=2;
	min_span*=2;		min_span*=2;
	@@ -7437,6 +7524,7 @@ y=xy0[1] + dUdeltaUV[0](xy1[1]-xy0[1])+dVdeltaUV[1](xy2[1]-xy0[1])
	thisWindow=window4;		thisWindow=window4;
	}		}
	}		}
			*/
	setCorrelationSizesUsed(thisCorrelationSize);		setCorrelationSizesUsed(thisCorrelationSize);
	if ((debug_level>0)&&(thisCorrelationSize>distortionParameters.correlationSize)) System.out.println("**** u/v span too small, increasing FFT size to "+thisCorrelationSize);		if ((debug_level>0)&&(thisCorrelationSize>distortionParameters.correlationSize)) System.out.println("**** u/v span too small, increasing FFT size to "+thisCorrelationSize);
	Rectangle centerCross=correlationSelection(		Rectangle centerCross=correlationSelection(
	@@ -7499,6 +7587,10 @@ y=xy0[1] + dUdeltaUV[0](xy1[1]-xy0[1])+dVdeltaUV[1](xy2[1]-xy0[1])
	thisCorrelationSize, // number of Bayer cells in width of the square selection (half number of pixels)		thisCorrelationSize, // number of Bayer cells in width of the square selection (half number of pixels)
	0,		0,
	0);		0);
			if (sim_pix==null){
			System.out.println("*** BUG: extractSimulPatterns() FAILED ***");
			return null;
			}

	simGreensCentered= normalizeAndWindow (sim_pix[4], thisWindow);		simGreensCentered= normalizeAndWindow (sim_pix[4], thisWindow);

	@@ -8966,6 +9058,7 @@ error=Sum(W(x,y)(F^2 + 2F(Ax^2+By^2+Cxy+Dx+E*y-Z(x,y)) +(...) )

	public static class DistortionParameters {		public static class DistortionParameters {
	public int correlationSize;		public int correlationSize;
			public int maximalCorrelationSize;
	public double correlationGaussWidth; // 0 - no window, <0 - use Hamming		public double correlationGaussWidth; // 0 - no window, <0 - use Hamming
	public boolean absoluteCorrelationGaussWidth=false; // do not scale correlationGaussWidth when the FFT size is increased		public boolean absoluteCorrelationGaussWidth=false; // do not scale correlationGaussWidth when the FFT size is increased
	public int zeros; // leave this number of zeros on the margins of the window (toatal from both sides). If correlationGaussWidth>0 will		public int zeros; // leave this number of zeros on the margins of the window (toatal from both sides). If correlationGaussWidth>0 will
	@@ -9027,6 +9120,7 @@ error=Sum(W(x,y)(F^2 + 2F(Ax^2+By^2+Cxy+Dx+E*y-Z(x,y)) +(...) )

	public DistortionParameters(		public DistortionParameters(
	int correlationSize,		int correlationSize,
			int maximalCorrelationSize,
	double correlationGaussWidth,		double correlationGaussWidth,
	boolean absoluteCorrelationGaussWidth,		boolean absoluteCorrelationGaussWidth,
	int zeros,		int zeros,
	@@ -9082,6 +9176,7 @@ error=Sum(W(x,y)(F^2 + 2F(Ax^2+By^2+Cxy+Dx+E*y-Z(x,y)) +(...) )
	){		){

	this.correlationSize = correlationSize;		this.correlationSize = correlationSize;
			this.maximalCorrelationSize=maximalCorrelationSize;
	this.correlationGaussWidth = correlationGaussWidth;		this.correlationGaussWidth = correlationGaussWidth;
	this.absoluteCorrelationGaussWidth=absoluteCorrelationGaussWidth;		this.absoluteCorrelationGaussWidth=absoluteCorrelationGaussWidth;
	this.zeros=zeros;		this.zeros=zeros;
	@@ -9139,6 +9234,7 @@ error=Sum(W(x,y)(F^2 + 2F(Ax^2+By^2+Cxy+Dx+E*y-Z(x,y)) +(...) )
	public DistortionParameters clone() {		public DistortionParameters clone() {
	return new DistortionParameters(		return new DistortionParameters(
	this.correlationSize,		this.correlationSize,
			this.maximalCorrelationSize,
	this.correlationGaussWidth,		this.correlationGaussWidth,
	this.absoluteCorrelationGaussWidth,		this.absoluteCorrelationGaussWidth,
	this.zeros,		this.zeros,
	@@ -9196,6 +9292,7 @@ error=Sum(W(x,y)(F^2 + 2F(Ax^2+By^2+Cxy+Dx+E*y-Z(x,y)) +(...) )

	public void setProperties(String prefix,Properties properties){		public void setProperties(String prefix,Properties properties){
	properties.setProperty(prefix+"correlationSize",this.correlationSize+"");		properties.setProperty(prefix+"correlationSize",this.correlationSize+"");
			properties.setProperty(prefix+"maximalCorrelationSize",this.maximalCorrelationSize+"");
	properties.setProperty(prefix+"correlationGaussWidth",this.correlationGaussWidth+"");		properties.setProperty(prefix+"correlationGaussWidth",this.correlationGaussWidth+"");
	properties.setProperty(prefix+"absoluteCorrelationGaussWidth",this.absoluteCorrelationGaussWidth+"");		properties.setProperty(prefix+"absoluteCorrelationGaussWidth",this.absoluteCorrelationGaussWidth+"");
	properties.setProperty(prefix+"zeros",this.zeros+"");		properties.setProperty(prefix+"zeros",this.zeros+"");
	@@ -9254,6 +9351,8 @@ error=Sum(W(x,y)(F^2 + 2F(Ax^2+By^2+Cxy+Dx+E*y-Z(x,y)) +(...) )
	public void getProperties(String prefix,Properties properties){		public void getProperties(String prefix,Properties properties){
	if (properties.getProperty(prefix+"correlationSize")!=null)		if (properties.getProperty(prefix+"correlationSize")!=null)
	this.correlationSize=Integer.parseInt(properties.getProperty(prefix+"correlationSize"));		this.correlationSize=Integer.parseInt(properties.getProperty(prefix+"correlationSize"));
			if (properties.getProperty(prefix+"maximalCorrelationSize")!=null)
			this.maximalCorrelationSize=Integer.parseInt(properties.getProperty(prefix+"maximalCorrelationSize"));
	if (properties.getProperty(prefix+"correlationGaussWidth")!=null)		if (properties.getProperty(prefix+"correlationGaussWidth")!=null)
	this.correlationGaussWidth=Double.parseDouble(properties.getProperty(prefix+"correlationGaussWidth"));		this.correlationGaussWidth=Double.parseDouble(properties.getProperty(prefix+"correlationGaussWidth"));
	if (properties.getProperty(prefix+"FFTSize")!=null)		if (properties.getProperty(prefix+"FFTSize")!=null)

src/main/java/SimulationPattern.java

+7 −1

Original line number	Original line	Diff line number	Diff line
	@@ -877,7 +877,13 @@ Cv=(Cyx-Cxy)+(-CyDx+CxDy)
	s=0.0;		s=0.0;
	for (py=iy0+sampLow;py<iy0+sampHigh;py++) for (px=ix0+sampLow;px<ix0+sampHigh;px++) {		for (py=iy0+sampLow;py<iy0+sampHigh;py++) for (px=ix0+sampLow;px<ix0+sampHigh;px++) {
	/// s+=this.barray[py][px];		/// s+=this.barray[py][px];
			try {
	s+=this.barray[py*fullSize+px];		s+=this.barray[py*fullSize+px];
			} catch (Exception e){
			System.out.println("Bug in extractSimulPatterns(): px="+px+" py="+py+" fullSize="+fullSize+" size="+size+" x0="+x0+" y0="+y0);
			e.printStackTrace();
			return null;
			}
	}		}
	simul_pixels[n][iy*size+ix]= (s-sampleAverage)/sampleAverage;		simul_pixels[n][iy*size+ix]= (s-sampleAverage)/sampleAverage;
	}		}

Original line number	Original line	Diff line number	Diff line
	@@ -302,6 +302,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene

	public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSimulatedPattern.DistortionParameters(		public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSimulatedPattern.DistortionParameters(
	64, //32, // use 64 for less artifacts, // correlationSize		64, //32, // use 64 for less artifacts, // correlationSize
			64, // Maximal correlation size
	0.75,// reduce to 0.5 when correlationSize==64 // correlationGaussWidth		0.75,// reduce to 0.5 when correlationSize==64 // correlationGaussWidth
	false, // boolean absoluteCorrelationGaussWidth=false; // do not scale correlationGaussWidth when the FFT size is increased		false, // boolean absoluteCorrelationGaussWidth=false; // do not scale correlationGaussWidth when the FFT size is increased
	0, //zeros - // leave this number of zeros on the margins of the window (toatal from both sides). If correlationGaussWidth>0 will		0, //zeros - // leave this number of zeros on the margins of the window (toatal from both sides). If correlationGaussWidth>0 will
	@@ -19190,6 +19191,8 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	gd.addNumericField("FFTSize (Initial pattern detection only):", distortionParameters.FFTSize, 0); // 128		gd.addNumericField("FFTSize (Initial pattern detection only):", distortionParameters.FFTSize, 0); // 128
	gd.addNumericField("FFT Gaussian width (relative):", distortionParameters.fftGaussWidth, 3);		gd.addNumericField("FFT Gaussian width (relative):", distortionParameters.fftGaussWidth, 3);
	gd.addNumericField("Correlation size:", distortionParameters.correlationSize, 0); // 64		gd.addNumericField("Correlation size:", distortionParameters.correlationSize, 0); // 64
			gd.addNumericField("Maximal correlation size:", distortionParameters.maximalCorrelationSize, 0); // 64

	gd.addNumericField("Correlation Gauss width (relative):", distortionParameters.correlationGaussWidth, 3);		gd.addNumericField("Correlation Gauss width (relative):", distortionParameters.correlationGaussWidth, 3);
	gd.addCheckbox("Keep Gaussian width absolute when increasing FFT size",distortionParameters.absoluteCorrelationGaussWidth);		gd.addCheckbox("Keep Gaussian width absolute when increasing FFT size",distortionParameters.absoluteCorrelationGaussWidth);
	// /phaseCorrelationFraction		// /phaseCorrelationFraction
	@@ -19268,6 +19271,8 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	distortionParameters.fftGaussWidth= gd.getNextNumber();		distortionParameters.fftGaussWidth= gd.getNextNumber();
	distortionParameters.correlationSize=1;		distortionParameters.correlationSize=1;
	for (i=(int) gd.getNextNumber(); i >1; i>>=1) distortionParameters.correlationSize <<=1; /* make it to be power of 2 */		for (i=(int) gd.getNextNumber(); i >1; i>>=1) distortionParameters.correlationSize <<=1; /* make it to be power of 2 */
			distortionParameters.maximalCorrelationSize=1;
			for (i=(int) gd.getNextNumber(); i >1; i>>=1) distortionParameters.maximalCorrelationSize <<=1; /* make it to be power of 2 */
	distortionParameters.correlationGaussWidth= gd.getNextNumber();		distortionParameters.correlationGaussWidth= gd.getNextNumber();
	distortionParameters.absoluteCorrelationGaussWidth=gd.getNextBoolean();		distortionParameters.absoluteCorrelationGaussWidth=gd.getNextBoolean();
	distortionParameters.zeros= (int) gd.getNextNumber();		distortionParameters.zeros= (int) gd.getNextNumber();

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