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88 lines
4.4 KiB
Matlab
88 lines
4.4 KiB
Matlab
% MAKE_SYNTHETIC_PROJECTIONS creates projections that can be used as
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% initial guess for ptychography reconstruction in order to solver
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% iterativelly the ptychotomo task
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%
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% merged = make_synthetic_projections(stack_object, sinogram_abs, sinogram_phase,total_shift,object_ROI)
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%
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% Inputs:
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% **stack_object - measured projections
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% **sinogram_abs - aligned absorbtion sinogram
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% **sinogram_phase - aligned phase sinogram
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% **total_shift - reconstructed shifts oft the measured projections
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% **object_ROI - reliable region of the projections
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% Outputs:
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% merged - merged projections using stack_object, sinogram_abs and sinogram_phase
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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 merged = make_synthetic_projections(stack_object, sinogram_abs, sinogram_phase,total_shift,object_ROI)
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[Nlayers,Nw,~] = size(sinogram_abs);
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Npx_proj = [size(stack_object,1),size(stack_object,2)];
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assert(length(object_ROI{1}) == Nlayers && length(object_ROI{2}) == Nw, 'Reconstructed tomograms have to contain the full field of view, ie vert_range = object_ROI{1}' )
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if isreal(sinogram_abs) && isreal(sinogram_phase)
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sinogram_abs = exp(-sinogram_abs);
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sinogram_phase = exp(-1i*sinogram_phase);
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else
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sinogram_phase = sinogram_abs ./ (abs(sinogram_abs)+1e-3);
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sinogram_abs = abs(sinogram_abs);
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end
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% find reliability region
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win = tukeywin(Nw, 0.2)'.*tukeywin(Nlayers, 0.2);
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win = utils.crop_pad(win, Npx_proj);
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% find amplitude correction
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corr = math.sum2(abs(stack_object(object_ROI{:},:)) .* sinogram_abs) ./ math.sum2(sinogram_abs.^2);
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% merge phase and amplitude from tomo and measurements
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merged = win.*utils.crop_pad(sinogram_phase,Npx_proj) + (1-win).*stack_object ./ (abs(stack_object)+1e-2);
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% enforce phasor
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merged = merged ./ (abs(merged) + 1e-2);
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% apply amplitude
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merged = merged .* ((win .* corr .* utils.crop_pad(sinogram_abs,Npx_proj) + (1-win).* abs(stack_object)));
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clear sinogram_phase sinogram_abs
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if ~isempty(total_shift)
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% apply shift to match the original data
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merged = utils.imshift_fft(merged, -total_shift);
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end
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end
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