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131 lines
8.8 KiB
Matlab
131 lines
8.8 KiB
Matlab
%C_SOLVER external C++ code for DM in lower resolution
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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 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 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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% 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 [ p , fdb] = presolver( p )
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import utils.interpolateFT
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scale = p.asize ./ p.asize_presolve;
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assert(scale(1) == scale(2), 'Nonequal probe size is not supported');
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assert(~p.prepare.legacy, 'Presolver with prepare.legacy option is not implemented')
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p_small = p;
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p_small. asize = p.asize_presolve; % size of the small reconstruction
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p_small. prepare_data_filename = [];
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p_small. prefix = 'presolver_';
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p_small. run_name = [p_small.prefix core.generate_scan_name(p) '_' num2str(p_small.asize(1)) 'x' num2str(p_small.asize(2)) '_' p.suffix]; % If empty: automatically generated
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p_small. plot.prepared_data = false; % plot prepared data
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p_small. save.store_images = false; % Write nice jpegs in [p.base_path,'analysis/online/ptycho/'] if p.use_display = 0 then the figures are opened invisible in order to create the nice layout. It writes images in analysis/online/ptycho
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p_small. plot.positions = false; % Plot the scanning positions
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p_small. plot.mask_bool = false; % Mask the noisy contour of the reconstructed object in plots
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p_small = rmfield(p_small, 'ds'); % avoid complains of the initialization code
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p_small = rmfield(p_small, 'object'); % remove before new initalization
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p_small = rmfield(p_small, 'detectors'); % remove before new initalization
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% p_small.fmag = utils.crop_pad(p_small.fmag, p.asize_presolve);
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% p_small.fmask = utils.crop_pad(p_small.fmask, p.asize_presolve);
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% p_small.prepare.auto_prepare_data = false;
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p_small.fmag = [];
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p_small.fmask = [];
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if isfield(p_small, 'prepare.legacy_filename')
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p_small.prepare.legacy_filename = replace(p_small.prepare.legacy_filename, sprintf('%ix%i', p.asize), sprintf('%ix%i', p_small.asize));
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end
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% load data nad other settings for small probe
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[p_small, status] = core.initialize_ptycho(p_small);
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% rescale the input estimates to presolver resolution
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p_small.probes = interpolateFT(p_small.probes,p_small.asize) ;
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for ii = 1:length(p_small.object)
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p_small.object{ii} = interpolateFT(p.object{1}, ceil(p_small.object_size(ii,:) ) );
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end
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% avoid ML code !!!
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p_small.opt_iter = 0;
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% run low resolution presolver
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[p_small, fdb] = engines.c_solver(p_small);
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% rescale the input estimates to final resolution
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p.probes = interpolateFT(p_small.probes,p.asize) ;
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for ii = 1:length(p_small.object)
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p.object{ii} = interpolateFT(p_small.object{ii},p.object_size(ii,:));
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end
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%% renormalize the probe and objects
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pnorm = math.norm2(p.probes);
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if p.share_object
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pnorm = mean(pnorm);
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end
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p.probes = p.probes / pnorm;
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for ii = 1:length(p.object)
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p.object{ii} = p.object{ii} * pnorm(p.share_object_ID(ii));
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end
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if isfield(p_small, 'error_metric')
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p.error_metric = p_small.error_metric;
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else
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p.error_metric = [];
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end
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p = rmfield(p, 'asize_presolve');
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end |