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170 lines
10 KiB
Matlab
170 lines
10 KiB
Matlab
% MODULUS_CONSTRAINT universal fast relaxed modulus constraint for amplitude and poission likelihood
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%
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% [chi,R] = modulus_constraint(modF,aPsi ,Psi, mask, noise, relax_noise,likelihood , R_offset)
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%
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% ** modF pre-fftshifted and sqrt-ed data
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% ** aPsi reciprocal amplitude model
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% ** Psi where Psi is the propagated exitwave
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% ** mask masked values, 1 = ignored, 0 = use this pixel
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% ** noise estimated noise (STD) in each pixel after sqrt transform
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% ** relax_noise multiplicative constant for the providede noise value
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% ** likelihood L1 or poisson
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% ** R_offset number to be subtracted from the modF / aPsi ratio
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%
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% returns:
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% ++ chi the updated wavefront or wavefront update, depends on the chosen R_offset
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% ++ R modF / aPsi ratio
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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 cSAXS
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% ptychography MATLAB package 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 cSAXS ptychography MATLAB 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 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 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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% for LSQ-ML method
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% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
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% for OPRP method
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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." Optics express 24.8 (2016): 8360-8369
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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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% 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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%
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%
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function [chi,R] = modulus_constraint(modF,aPsi ,Psi, mask, noise, par, R_offset)
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import engines.GPU.GPU_wrapper.*
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likelihood = lower(par.likelihood);
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relax_noise = par.relax_noise;
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Nmodes = length(Psi);
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R = [];
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if par.upsampling_data_factor
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% calculate the convolution with delta functions
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modF = utils.unbinning_2D(modF, 2^par.upsampling_data_factor );
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aPsi = utils.unbinning_2D(aPsi, 2^par.upsampling_data_factor );
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if ~isempty(mask) && ~isscalar(mask)
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mask = utils.unbinning_2D(mask, 2^par.upsampling_data_factor );
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end
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end
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%% write the most common cases as merged kernels
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if nargout == 1
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if isempty(mask) && isempty(noise) && relax_noise == 0 && strcmpi(likelihood, 'l1') && Nmodes == 1 % common modulus constraint
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chi{1} = Gfun(@modulus_non_relaxed,Psi{1},modF, aPsi, R_offset);
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return
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end
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if ~isempty(mask) && isempty(noise) && strcmpi(likelihood, 'l1') && Nmodes == 1 % common modulus constraint
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chi{1} = Gfun(@modulus_weight_relaxed,Psi{1},modF, aPsi,mask, R_offset);
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return
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end
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end
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if isempty(mask) && isempty(noise) && relax_noise == 0 % common modulus constraint
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switch likelihood
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case 'l1', R = Gfun(@non_relaxed, modF, aPsi, R_offset);
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case 'poisson', R = Gfun(@poisson_noise_relaxed,modF, aPsi, R_offset);
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end
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elseif isempty(mask) && isempty(noise) && relax_noise > 0 % common modulus constraint
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switch likelihood
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case 'l1', R = Gfun(@weight_relaxed, modF, aPsi, relax_noise, R_offset );
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case 'poisson', R = Gfun(@poisson_noise_weight_relaxed,modF, aPsi,relax_noise, R_offset);
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end
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elseif ~isempty(mask) && isempty(noise)
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switch likelihood
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case 'l1', R = Gfun(@weight_relaxed, modF, aPsi, max(mask, relax_noise), R_offset );
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case 'poisson', R = Gfun(@poisson_noise_weight_relaxed,modF, aPsi, max(mask, relax_noise), R_offset);
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end
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elseif isempty(mask) && ~isempty(noise)
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R = Gfun(@noise_relaxed, modF, aPsi, noise, relax_noise, R_offset);
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else
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R = Gfun(@noise_weight_relaxed, modF, aPsi, noise,relax_noise, mask, R_offset);
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end
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for i = 1:Nmodes
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chi{i} = Psi{i} .* R; % apply the constraint to the currect estimation
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end
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end
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% classical modulus
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function chi = modulus_non_relaxed(Psi,modF, aPsi, R_offset)
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R = (modF./(aPsi+1e-9)- R_offset);
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chi = R .* Psi;
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end
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function chi = modulus_weight_relaxed(Psi,modF, aPsi,W, R_offset)
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R = (W+(1-W).*modF./(aPsi+1e-9))- R_offset;
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chi = R .* Psi;
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end
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function R = non_relaxed(modF, aPsi, R_offset)
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R = modF./(aPsi+1e-9)- R_offset;
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end
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% modulus for noisy data with relaxation
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function R = weight_relaxed(modF, aPsi, W, R_offset)
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R = (W+(1-W).*modF./(aPsi+1e-9))- R_offset;
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end
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function R = noise_relaxed(modF, aPsi, noise, relax_noise, R_offset)
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W = 1 ./ (1+ ((aPsi - modF)./(noise .* relax_noise)).^2 );
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R = (W+(1-W).*modF./(aPsi+1e-9))- R_offset;
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end
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function R = noise_weight_relaxed(modF, aPsi, noise,relax_noise, W0, R_offset)
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% if mask == 1 then W has to be 0
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W = 1-(1-W0) .* (1-1./ (1+ ((aPsi - modF)./(noise .* relax_noise) ).^2 ));
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R = (W+(1-W).*modF./(aPsi+1e-9))- R_offset;
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end
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function R = poisson_noise_weight_relaxed(modF, aPsi, W, R_offset)
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% if mask == 1 then W has to be 0
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% Maximum-likelihood refinement for coherent diffractive imaging
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R = (W+(1-W).*modF.^2 ./(aPsi.^2+1e-3))- R_offset;
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end
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function [R] = poisson_noise_relaxed(modF, aPsi, R_offset)
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% if mask == 1 then W has to be 0
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% Maximum-likelihood refinement for coherent diffractive imaging
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R = modF.^2 ./(aPsi.^2+1e-3)- R_offset;
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end
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