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86 lines
3.7 KiB
Matlab
86 lines
3.7 KiB
Matlab
% UNWRAP2D_FFT simple and very fast 1D phase unwrapping applied for each
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% slice of the provided image stack
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%
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% phase = unwrap2D_fft(img, axis, empty_region, step)
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%
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% Inputs:
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% **img - (2D or 3D image stack) either complex valued image or real valued phase gradient
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% **axis - (scalar, int) axis along which the gradient is taken
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% *optional*
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% **empty_region - 2x1 or 1x1 vector, size of empty region assumed around edges for phase offset removal, default=[]
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% **step - used to calculate finite difference gradient, 0 = analytical (default) expression
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%
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% *returns*
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% ++phase - unwrapped phase with phase ramp removed
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% ++phase_diff - if img is complex array, phase difference can be also returned
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% ++residues - calculated binary map of phase residuas
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%
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% See also: utils.findresidues, utils.remove_sinogram_ramp
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function [phase, phase_diff, residues] = unwrap2D_fft(phase_diff, axis, empty_region, step)
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import math.*
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import utils.*
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if nargin < 4
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step = 0;
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end
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if nargin < 3
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empty_region = [];
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end
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if nargout > 2 && ~isreal(phase_diff) % if input is complex array
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residues = abs(findresidues(phase_diff)) > 0.1;
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else
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residues = [];
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end
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if ~isreal(phase_diff)
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phase_diff = get_phase_gradient_1D(phase_diff, axis, step);
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end
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phase = real(get_img_int_1D(phase_diff,axis));
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if ~isempty(empty_region) && axis == 2
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phase = remove_sinogram_ramp(phase,empty_region,-1);
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end
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end
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