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%% TEST TEMPLATE FOR FUNTIONALITY CHECK IN GPU ENGINES
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% 1) call standard template to get fresh settings defaults
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% 2) generate artificial data that should serve as a standart test "sample"
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% 3) call GPU engine with different basic functionalities and test if all still works
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% !! THESE TEST ARE ONLY USEFUL TO FIND CRASHES IN THE CODE, QUALITY OF THE RECONSTRUCTION IS NOT EVALUATED !!
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%% set shared parameters for all test scripts
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run(fullfile( fileparts(mfilename('fullpath')), 'init_test.m'))
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%% general settings
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p. artificial_data_file = 'tests/test_data_camera_geometry.m'; % artificial data parameters
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p. asize = [128 128]; % size of the reconstruction probe
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p. preserve_previous_results = true;
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plot_results = true;
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%% ENGINES
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% --------- GPU engines -------------
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eng = struct();
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eng. name = 'GPU';
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eng. use_gpu = true; % if false, run CPU code, but it will get very slow
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eng. gpu_id = []; % default GPU id, [] means choosen by matlab
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%% general
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eng. share_probe = 0; % Share probe between scans. Can be either a number/boolean or a list of numbers, specifying the probe index; e.g. [1 2 2] to share the probes between the second and third scan.
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eng. grouping = inf; % size of processed blocks, larger blocks need more memory but they use GPU more effeciently
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% for hPIE, ePIE, MLs methods smaller blocks lead to faster convergence,
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eng_0 = eng;
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if 1
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%% presolve by DM solver
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eng = eng_0;
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eng. method = 'DM'; % choose GPU solver: DM, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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eng. number_iterations = 50; % number of iterations for selected method
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eng.probe_change_start = 5;
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eng. pfft_relaxation = 0.1; % Relaxation in the Fourier domain projection, = 0 for full projection
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eng. probe_regularization = 0.1;% Weight factor for the probe update (inertia)
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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end
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if 1
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%% presolve by MLc solver
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eng = eng_0;
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eng. method = 'MLc'; % choose GPU solver: DM, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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eng. number_iterations = 50; % number of iterations for selected method
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eng.probe_change_start = 1;
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eng. mirror_objects = true; % mirror objects, useful for 0/180deg scan sharing -> geometry refinement for tomography
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eng. share_object = false;
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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end
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if 1
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%% test geometry refinement with MLc solver
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eng = eng_0;
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eng. number_iterations =200; % number of iterations for selected method
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eng.probe_modes = 1;
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eng. method = 'MLc'; % choose GPU solver: DM, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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eng.grouping = inf;
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eng. mirror_objects = true; % mirror objects, useful for 0/180deg scan sharing -> geometry refinement for tomography
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eng. share_object = true;
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eng. detector_rotation_search = 10;
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eng. detector_scale_search = 10;
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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end
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run(fullfile( fileparts(mfilename('fullpath')), 'run_test.m'))
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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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