adapt scaling of x-axis in checkFresnelNumber

frequency axis is now scaled such the first minimum of the CTF is on 1
fix #3

functions/phaseRetrieval/utilities/checkFresnelNumber.m

@@ -82,28 +82,28 @@ hologram = fadeoutImage(hologram);
 hologramPSDAngularAvg = angularAverage(powerSpectralDensity(double(hologram)));
 
 % Fourier-frequencies corresponding to the PSD-values, normalized with Fresnel number
-fourierFreqs = fftfreq(size(hologram,1));
-fourierFreqs = fourierFreqs(1:ceil(end/2)) ./ sqrt(4*pi*fresnelNumberExpected);
+fourierFreqs = fftfreq(size(hologram,1), 2 * pi);
+fourierFreqs = fourierFreqs(1:ceil(end/2)) ./ (sqrt(fresnelNumberExpected));
 
 % Restrict the frequency range to the specified number of CTF-periods
-maxFreq = sqrt(2*pi*settings.maxNumPlottedCTFPeriods);
-hologramPSDAngularAvg = hologramPSDAngularAvg(fourierFreqs < maxFreq);
-fourierFreqs = fourierFreqs(fourierFreqs < maxFreq);
+maxFreq = sqrt(settings.maxNumPlottedCTFPeriods);
 
 % Compute expected contrast-transfer-function CTF with fine sampling 
-fourierFreqsCTF = linspace(0, min(pi./sqrt(4*pi*fresnelNumberExpected), maxFreq), 10000).';
-ctfExpected = (sin(fourierFreqsCTF.^2) + settings.betaDeltaRatio * cos(fourierFreqsCTF.^2)).^2;
+fourierFreqsCTF = linspace(0, 1.05 * maxFreq, 10000).';
+ctfExpected = (sin(pi * fourierFreqsCTF.^2) + settings.betaDeltaRatio * cos(pi * fourierFreqsCTF.^2)).^2;
 
 % Scale CTF for better visibility in joint plot with PSD
-minPSD = min(hologramPSDAngularAvg(:));
-maxPSDHighFreq = max(hologramPSDAngularAvg(fourierFreqs > sqrt(pi/2)));
+mask = (fourierFreqs < maxFreq) & (fourierFreqs > 0.25);
+minPSD = min(hologramPSDAngularAvg(mask));
+maxPSDHighFreq = max(hologramPSDAngularAvg(mask));
 ctfExpected = (maxPSDHighFreq./max(ctfExpected(:))) * ctfExpected;
 
 % Jointly plot computed PSD and expected CTF with logarithmic y-axis
 figure; plot(fourierFreqs, hologramPSDAngularAvg, '-b', fourierFreqsCTF, ctfExpected, '--r');
 set(gca, 'YScale', 'log');
 ylim([0.8*minPSD, 1.25*maxPSDHighFreq]);
-xlim([0, maxFreq]);
+xlim([0, 1.05 * maxFreq]);
+xlabel('k / F^{1/2}')
 legend({'PSD(hologram)', 'expected CTF'}, 'location', 'northeast');
 title(['Check that the location of the minima in the two curves coincide. ', ...
        'If the minima differ systematically, the entered Fresnel number is probably wrong']);