Add generalized paganin method as a new phase retrieval algorithm for the direct contrast regime

functions/phaseRetrieval/directContrast/phaserec_gpm.m

+function phase = phaserec_gpm(hologram, fresnelNumber, settings)
+%PHASEREC_GPM reconstructs the phase with the "Generalized Paganin Method" for homogeneous objects.
+%
+%    ``phase = phaserec_gpm(hologram, fresnelNumber, settings)``
+%
+% Reconstructed the phase in the object plane using the generalized paganin method proposed by Paganin et al. arXiv:2005.03660. It is valid for
+% short propagation distances and homogeneous objects.
+%
+% Parameters
+% ----------
+% hologram : numerical array
+%     hologram to reconstruct from
+% fresnelNumber : number
+%     pixel size-based Fresnel number
+% settings : structure, optional
+%     contains additional settings, see *Other Parameters*
+%
+% Other Parameters
+% ----------------
+% betaDeltaRatio : Default = 0.01
+%     Beta/Delta ratio
+% padx : Default = 0
+%     Amount by which the hologram is symmetrically (replicate)-padded along the
+%     x-dimension before reconstruction
+% pady : Default = 0
+%     Amount by which the hologram is symmetrically (replicate)-padded along the 
+%     y-dimension before reconstruction
+%
+% Returns
+% -------
+% phase : numerical array
+%     The reconstructed phase image of the same size as the input hologram
+%
+%
+% See also
+% --------
+% functions.phaseRetrieval.directContrast.phaserec_mba,
+% functions.phaseRetrieval.directContrast.phaserec_smo
+%
+% Example
+% -------
+%
+% .. code-block:: matlab
+%
+%     out = getHologram('spider');
+% 
+%     smosettings = phaserec_gpm;
+%     smosettings.padx = 100;
+%     smosettings.pady = 100;
+%     smosettings.betaDeltaRatio = 0.015;
+% 
+%     projReconstructed = phaserec_gpm(out.holograms, out.fresnelNumbers, smosettings);
+% 
+%     showImage(projReconstructed);
+% 
+% 
+% See also PHASEREC_MBA, PHASEREC_SMO
+
+% HoloTomoToolbox
+% Copyright (C) 2019  Institut fuer Roentgenphysik, Universitaet Goettingen
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+defaults.padx = 0;
+defaults.pady = 0;
+defaults.betaDeltaRatio = 0.01;
+
+if (nargin == 0)
+    phase = defaults;
+    return
+end
+
+if (nargin < 3)
+    settings = struct;
+end
+
+settings = completeStruct(settings, defaults);
+
+if (settings.betaDeltaRatio <= 0)
+    error('settings.betaDeltaRatio <= 0 given')
+end
+
+if (fresnelNumber <= 0)
+    error('fresnelNumber <= 0 given')
+end
+
+% optional paddding
+hologramPadded = padarray(hologram, [settings.pady settings.padx], 'replicate');
+
+% multplicative factor in Fourier space that correspond to the Laplacian in real space
+[xi_y, xi_x] = fftfreq(size(hologramPadded))
+
+% regularization of the Laplacian at zero frequency is determined by Fresnel number and absorption
+reg_alpha = 4 * pi * fresnelNumber * settings.betaDeltaRatio;
+
+% apply inverse filter to reconstruct the phase
+filterKernel = reg_alpha ./ (reg_alpha - 2 * (cos(xi_x) + cos(xi_y) - 2) );
+phase = 1/(2 * settings.betaDeltaRatio) * log(real(ifft2(fft2(hologramPadded).*filterKernel)));
+
+% undo padding 
+phase = croparray(phase, [settings.pady, settings.padx]);   
+   
+end
+

functions/phaseRetrieval/directContrast/phaserec_smo.m

@@ -106,8 +106,8 @@ laplaceKernel = -fftfreqNormSq(size(hologramPadded));
 reg_alpha = 4 * pi * fresnelNumber * settings.betaDeltaRatio;
 
 % apply inverse filter to reconstruct the phase
-filterKernel = 1 ./ (-laplaceKernel + reg_alpha);
-phase = 1/(2 * settings.betaDeltaRatio) * log(reg_alpha * real(ifft2(fft2(hologramPadded).*filterKernel)));
+filterKernel = reg_alpha ./ (-laplaceKernel + reg_alpha);
+phase = 1/(2 * settings.betaDeltaRatio) * log(real(ifft2(fft2(hologramPadded).*filterKernel)));
 
 % undo padding 
 phase = croparray(phase, [settings.pady, settings.padx]);