merged and resolved the conflict in readSpec.m

README.md

 # HoloTomoToolbox
 
+## How to cite ?
+
+when using this toolbox, please cite: 
+
+A phase-retrieval toolbox for X-ray holography and tomography
+Leon M. Lohse, Anna-Lena Robisch, Mareike Töpperwien, Simon Maretzke, Martin Krenkel, Johannes Hagemann, and Tim Salditt
+Journal of Synchrotron Radiation 27, 852-859 (2020).
+https://doi.org/10.1107/S1600577520002398 
+
 ## Documentation
 
 See the [online-documentation](https://irp.pages.gwdg.de/holotomotoolbox/) and code examples in [examples/](examples/).

functions/imageProcessing/alignment/rotateImage.m

@@ -67,6 +67,10 @@ function imTransformed = rotateImage(im, rotAngleDegree, settings)
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+if nargin == 0
+    imTransformed = rmfield(shiftRotateMagnifyImage, 'invertTransform');
+    return
+end
 if nargin < 3
     settings = struct;
 end

functions/imageProcessing/alignment/shiftImage.m

@@ -66,6 +66,10 @@ function imTransformed = shiftImage(im, shifts, settings)
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+if nargin == 0
+    imTransformed = rmfield(shiftRotateMagnifyImage, 'invertTransform');
+    return
+end
 if nargin < 3
     settings = struct;
 end

functions/imageProcessing/alignment/shiftRotateImage.m

@@ -87,6 +87,10 @@ function imTransformed = shiftRotateImage(im, shifts, rotAngleDegree, settings)
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+if nargin == 0
+    imTransformed = shiftRotateMagnifyImage;
+    return
+end
 if nargin < 4
     settings = struct;
 end

functions/imageProcessing/artefactRemoval/removeStripes.m

@@ -17,16 +17,14 @@ function [imCorr, corr2D] = removeStripes(imToCorr,settings)
 %
 % Other Parameters 
 % ---------------- 
-% rangeTop : Default = 1:100
-%     Range at the top of the image to average.
+% rangeTop : Default = []
+%     Range at the top of the image to average. [] results in the top most 4%
 % rangeBottom : Default = []
-%     Range at the bottom of the image to average. [] results in the bottom most 100
-%     pixels of the image.
-% rangeLeft : Default = 1:100
-%     Range at the left edge of the image to average.
+%     Range at the bottom of the image to average. [] results in the bottom most 4%
+% rangeLeft : Default = []
+%     Range at the left edge of the image to average. [] results in the left most 4%
 % rangeRight : Default = []
-%     Range at the right edge of the image to average. [] results in the right most
-%     100 pixels of the image.
+%     Range at the right edge of the image to average. [] results in the right most 4%
 % windowSize : Default = 5
 %     Window size for smoothing the profile via a moving mean.
 % direction : Default = 'vertical'

functions/inputOutput/readSpec.m

@@ -41,7 +41,6 @@ if(nargin < 2)
     % find available scans in specified file
     list_scans(file)
     return
-    error('Not enough input arguments: specify filepath, scan number and column');
 end
 
 if (nargin < 3)

functions/phaseRetrieval/holographic/phaserec_nonlinTikhonov.m

@@ -236,7 +236,8 @@ F = NonlinearPhaseContrastOperator(N, fresnelNumbers, parOp);
 % Tikhonov functional(f) = || F(f) - holograms ||_2^2 + 2*|| regWeights * fft2(f) ||_2^2,
 % where regWeights contains the same Fourier-space regularization weights as used in phaserec_ctf
 % (note that "*" denotes composition of Operators/functionals in the following statements)
-regWeightsTimes2 = 2*ctfRegWeights(N, mean(fresnelNumbers,2), settings.lim1, settings.lim2, useGPU);
+regWeightsTimes2 = 2*ctfRegWeights(N, mean(fresnelNumbers,2), settings.lim1, settings.lim2, ...
+                                   useGPU, 2*numHolos);
 TikhonovFunctional =   NormSqFunctional * (F - holograms) ...
                      + NormSqFunctional(@(f) real(ifft2(regWeightsTimes2 .* fft2(f))));
 

functions/phaseRetrieval/holographic/private/ctfRegWeights.m

-function regWeights = ctfRegWeights(sizeHolo, fresnelNumbers, lim1, lim2, gpuFlag)
+function regWeights = ctfRegWeights(sizeHolo, fresnelNumbers, lim1, lim2, gpuFlag, lim3)
 % Computes a regularization weights in Fourier space, suitable for regularized inversion
 % of the CTF and similar reconstruction methods. The main idea, originally proposed by
 % Peter Cloetens, is to create a mask that smoothly transitions from one (typically low) 
@@ -32,11 +32,27 @@ xi = cell([ndim,1]);
 [xi{:}] = fftfreq(sizeHolo, 1);
 XiSqDivFresnel = 0;
 for jj = 1:ndim
-    XiSqDivFresnel = XiSqDivFresnel + gpuArrayIf(xi{jj}, gpuFlag).^2 ./ (2*pi^2*fresnelNumbers(jj));
+    xi{jj} = gpuArrayIf(xi{jj}, gpuFlag);
+    XiSqDivFresnel = XiSqDivFresnel + xi{jj}.^2 ./ (2*pi^2*fresnelNumbers(jj));
 end
 
 sigma = (sqrt(2) - 1) / 2; 
 w = 1/2 * erfc((sqrt(XiSqDivFresnel) - 1) / (sqrt(2) * sigma));
 regWeights = lim1 .* w + lim2 .* (1 - w);
 
+% Additional regularization level for spatial frequencies beyond the 
+% numerical aperture of the optical system. Only relevant for
+% deeply holographic data
+if nargin == 6
+    fresnelNumbersFOV = fresnelNumbers(:) .* sizeHolo(:).^2;
+    freqCutoffFOV = pi .* (fresnelNumbersFOV./sizeHolo(:));
+    wCutoffFOV = 1;
+    XiSqDivCutoffFOV = 0;
+    for jj = 1:ndim
+        XiSqDivCutoffFOV = XiSqDivCutoffFOV + (xi{jj}./freqCutoffFOV(jj)).^2;
+        wCutoffFOV = wCutoffFOV .* (0.5 .* erfc((abs(xi{jj})./freqCutoffFOV(jj)-1)./0.1));
+    end
+    regWeights = wCutoffFOV .* regWeights + (1-wCutoffFOV) .* lim3;
+end
+
 end