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https://github.com/c-sooyoung/fold_slice.git
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138 lines
8.3 KiB
Matlab
138 lines
8.3 KiB
Matlab
%% Prepare the reconstruction
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if ~exist('eng', 'var')
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return % return if no engine is provided
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end
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fprintf('Creating dataset .... ')
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[p, status] = core.ptycho_recons(p, true);
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if status && all(isfinite(p.fmag(:))) && all(isfinite(p.object{1}(:))) && all(isfinite(p.probes(:)))
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fprintf('OK\n')
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else
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error('Data creator failed, quitting ... ')
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end
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p. plot.windowautopos = true; % distribute the plotted windows
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p. plot.remove_phase_ramp = true;
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p_0 = p; % store the initial p-structure
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%% get all engines
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utils.verbose(struct('prefix', {'ptycho'}))
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for ieng=1:length(p.engines)
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if ~check_option(p, 'preserve_previous_results')
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p = p_0;
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end
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p.current_engine_id = ieng;
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% engine call
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if ~isfield(p.engines{ieng}, 'method'); p.engines{ieng}.method = '' ;end
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fprintf('Testing engine "%s" using method "%s" .... ', p.engines{ieng}.name, p.engines{ieng}.method)
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utils.verbose(struct('prefix', {p.engines{ieng}.name}))
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try
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t_start = tic;
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[p, fdb] = core.run_engine(p, ieng);
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if p.ortho_probes && size(p.probes,4)>1
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% orthogonalize probes
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p.probes = core.probe_modes_ortho(p.probes);
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end
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warning on
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warning off backtrace
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if fdb.status.status ~= 0
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fprintf('failed\n')
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warning('Engine %s returned with exit status %d from %s [%d].\n', p.engines{ieng}.name, fdb.status.status, fdb.status.ln(1).name, fdb.status.ln(1).line);
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elseif any(~isfinite(p.object{1}(:))) || any(~isfinite(p.probes(:)))
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warning('Engine %s returned non finite values in reconstrutions',p.engines{ieng}.name)
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else
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fprintf('OK \tTime: %3.2gs\n', (toc(t_start)))
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p.plot.extratitlestring = sprintf('engine "%s" using method "%s"', p.engines{ieng}.name, p.engines{ieng}.method);
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if plot_save_results && plot_results
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p.use_display = true;
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p.save.save_reconstructions = false; % prevent writting to disk
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[p] = core.save.save_results(p, true);
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elseif plot_results && ~plot_save_results
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core.analysis.plot_results(p)
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elseif plot_save_results
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p.use_display = false;
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p.save.save_reconstructions = false; % prevent writting to disk
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[p] = core.save.save_results(p, true);
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p.use_display = true;
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end
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end
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catch err
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fprintf(1, 'failed\n')
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warning(err.getReport)
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end
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end
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% delete temporal data
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for path = p.save_path
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rmdir(path{1}, 's')
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end
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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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