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irp
HoloTomoToolbox
Commits
7104c33a
Commit
7104c33a
authored
Jun 15, 2020
by
Leon Merten Lohse
Browse files
Add generalized paganin method as a new phase retrieval algorithm for the direct contrast regime
parent
82235c9d
Pipeline
#139715
passed with stage
in 1 minute and 48 seconds
Changes
2
Pipelines
1
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Inline
Side-by-side
functions/phaseRetrieval/directContrast/phaserec_gpm.m
0 → 100755
View file @
7104c33a
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
View file @
7104c33a
...
...
@@ -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
]);
...
...
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