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149 lines
9.6 KiB
Matlab
149 lines
9.6 KiB
Matlab
%PREPARE_PROJECTIONS, use ptycho reconstruction object_0 and initial guess
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%object_guess_c to calculate updated linearized complex object_c, i.e. object_0 = exp(object_c)
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% -> projections needs to be unwrapped
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%
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% object_c = prepare_projections(object_0, Npx_proj, probe_size, merge_layers, object_guess_c, weight)
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%
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% Inputs:
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% **object_0 - stack of 2D reconstructed layers from ptychography
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% **Npx_proj - size of the tomography projections
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% **probe_size - p.asize value
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% **merge_layers - bool, if true, merge all layers to one before unwrapping
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% **object_guess_c - stack of 2D layers used as initial guess for from ptychography
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% **weight - array denoting reliability for different regions of object_0 array
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%
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% *returns*
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% ++object_c - linearized complex projection, ie object_0 = exp(object_c)
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% Academic License Agreement
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%
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% Source Code
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%
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% Introduction
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% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
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% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the PtychoShelves
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% computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
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%
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% Terms and Conditions of the LICENSE
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% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
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% hereinafter set out and until termination of this license as set forth below.
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% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
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% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
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% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
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% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
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% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
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% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
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% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
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% in the commercial use, application or exploitation of works similar to the PROGRAM.
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% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
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% another computing language:
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% "Data processing was carried out using the PtychoShelves package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
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% Scherrer Institut, Switzerland."
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%
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% Additionally, any publication using the package, or any translation of the code into another computing language should cite
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% K. Wakonig, H.-C. Stadler, M. Odstrčil, E.H.R. Tsai, A. Diaz, M. Holler, I. Usov, J. Raabe, A. Menzel, M. Guizar-Sicairos, PtychoShelves, a versatile
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% high-level framework for high-performance analysis of ptychographic data, J. Appl. Cryst. 53(2) (2020). (doi: 10.1107/S1600576720001776)
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% and for difference map:
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% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
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% (doi: 10.1126/science.1158573),
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% for maximum likelihood:
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% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
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% (doi: 10.1088/1367-2630/14/6/063004),
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% for LSQ-ML:
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% M. Odstrčil, A. Menzel, and M. Guizar-Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Opt. Express 26(3), 3108 (2018).
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% (doi: 10.1364/OE.26.003108),
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% for mixed coherent modes:
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% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
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% and/or for multislice:
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% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
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% (doi: 10.1364/OE.24.029089),
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% and/or for OPRP:
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% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, Ptychographic coherent diffractive imaging with orthogonal probe relaxation.
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% Opt. Express 24.8 (8360-8369) 2016. (doi: 10.1364/OE.24.008360).
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% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
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% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
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% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
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% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
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% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
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% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
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% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
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% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
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% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
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% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
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% the courts of Zürich, Switzerland.
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function object_c = prepare_projections(object_0, Npx_proj, probe_size, merge_layers, object_guess_c, weight)
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% get updated unwrapped object_c given the new object estiamte and the original unwrapped
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% object before the ptycho iteration
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if nargin < 4
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merge_layers = false;
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end
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%% smoothly merge with the last reconstruction at this angle
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object_0 = utils.crop_pad(object_0,Npx_proj(1:2));
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if nargin > 4 && ~isempty(object_guess_c)
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% get only difference from the previous and then use this for
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% unwrapping
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object_guess = exp(object_guess_c);
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object = (object_0 .* conj(object_guess)) ./ (1e-4+abs(object_guess).^2);
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clear object_guess
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else
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object = object_0;
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end
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%% multilayer expantion
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% find reliability region
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if merge_layers
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object = prod(object,3);
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end
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win = tukeywin(Npx_proj(2), probe_size(2)/Npx_proj(2)/2)'.*tukeywin(Npx_proj(1), probe_size(1)/Npx_proj(1)/2);
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%% empirical way to estimate the unwrapping region
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weight = utils.Garray(weight .* win);
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if ~isempty(object_guess_c)
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Niter_unwrap = 3; % assume that initial guess is good enough
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else
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Niter_unwrap = 10; % try more iterations in the first step
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end
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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unwrapped_phase = tomo.unwrap2D_fft2_split(object ,[],0, weight, [], [], [], Niter_unwrap);
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attenuation = log(max(1e-1,abs(object_0)));
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if ~isempty(object_guess_c)
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% make the fit exact, maybe not needed , useful when the update changes are small
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unwrapped_phase = unwrapped_phase + angle(object .* exp(-1i*unwrapped_phase)) .* weight;
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% limit maximal absorbtion to 90% and tranmission to 100%
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object_c = complex(attenuation, imag(object_guess_c)+unwrapped_phase);
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else
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object_c = complex(attenuation , unwrapped_phase);
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end
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% zero the empty regions
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object_c = object_c .* (object_0 ~= 0);
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if merge_layers
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object_c = repmat(object_c,1,1,Npx_proj(3))/Npx_proj(3);
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end
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end
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