%% TEST TEMPLATE FOR FUNTIONALITY CHECK IN GPU ENGINES % 1) call standard template to get fresh settings defaults % 2) generate artificial data that should serve as a standart test "sample" % 3) call GPU engine with different basic functionalities and test if all still works % !! THESE TEST ARE ONLY USEFUL TO FIND CRASHES IN THE CODE, QUALITY OF THE RECONSTRUCTION IS NOT EVALUATED !! %% set shared parameters for all test scripts run(fullfile( fileparts(mfilename('fullpath')), 'init_test.m')) plot_results = true; %% general settings p. artificial_data_file = 'tests/test_data_mirror_objects.m'; % artificial data parameters p. asize = [256 256]; % size of the reconstruction probe p. scan.lx = 10e-6; % round_roi scan: width of the roi p. scan.ly = 10e-6; p. preserve_previous_results = true; % do not reset p-struct after the first reconstruction %% ENGINES % External C++ code % --------- GPU engines ------------- if 1 eng = struct(); eng. name = 'GPU'; eng. use_gpu = true; % if false, run CPU code, but it will get very slow eng. keep_on_gpu = true; % keep data + projections on GPU, false is useful for large data if DM is used eng. compress_data = true; % use automatic online memory compression to limit meed of GPU memory eng. gpu_id = []; % default GPU id, [] means choosen by matlab eng. check_gpu_load = true; % check available GPU memory before starting GPU engines %% general eng. number_iterations = 20; % number of iterations for selected method %eng. share_probe = 1; % 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. %eng. share_object = 0; % Share object between scans. Can be either a number/boolean or a list of numbers, specifying the object index; e.g. [1 2 2] to share the objects between the second and third scan. eng. method = 'MLs'; % choose GPU solver: DM, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs eng. opt_errmetric = 'L1' ; % optimization likelihood - poisson, L1 eng. grouping = 50; % size of processed blocks, larger blocks need more memory but they use GPU more effeciently % for hPIE, ePIE, MLs methods smaller blocks lead to faster convergence, % for pPIE, MLc the convergence is similar % for DM, RAAR is has no effect on convergence %eng. probe_modes = 1; % Number of coherent modes for probe eng. object_change_start = 1; % Start updating object at this iteration number eng. probe_change_start = 1; % Start updating probe at this iteration number eng.probe_support_fft = false; % regularizations eng. reg_mu = 0; % Regularization constant ( = 0 for no regularization) eng. delta = 0; % press values to zero out of the illumination area, usually 1e-2 is enough eng. positivity_constraint_object = 0; % enforce weak positivity in object, usually 1e-2 is already enough eng. apply_multimodal_update = false; % apply all incoherent modes to object, it can cause isses if the modes collect some crap eng. probe_backpropagate = 0; % backpropagate the probe mask, inf == farfield % basic recontruction parameters % PIE / ML methods eng. beta_object = 1; % object step size, larger == faster convergence, smaller == more robust, should not exceed 1 eng. beta_probe = 1; % probe step size, larger == faster convergence, smaller == more robust, should not exceed 1 eng. delta_p = 0.1; % LSQ dumping constant, 0 == no preconditioner, 0.1 is usually safe, % DM eng. pfft_relaxation = 0.1; % Relaxation in the Fourier domain projection, = 0 for full projection eng. probe_regularization = 0.1;% Weigth factor for the probe update (inertia) % ADVANCED OPTIONS % position refinement eng. apply_subpix_shift = false; % apply FFT-based subpixel shift, important for good position refinement but it is slow eng. probe_position_search = inf; % reconstruct probe positions, from iteration == probe_pos_search, assume they are independed eng. probe_position_error_max = 10e-9; % max expected random position error of the stages % wavefront refinement eng. probe_fourier_shift_search = inf; % refine farfield position of the beam (ie angle) from iteration == probe_fourier_shift_search eng. estimate_NF_distance = inf; % try to estimate the nearfield propagation distance eng. variable_probe = false; % Use SVD to account for variable illumination during a single (coupled) scan eng. variable_SVD_modes = 3; % OPRP settings , number of SVD modes, apply only for PIE methods eng. variable_probe_smooth = 0; % OPRP settings , apply assumption of smooth evolution of the OPRP modes (ie slow drifts) eng. variable_intensity = false; % account to changes in probe intensity %% test MLc/s codes eng. method = 'MLs'; % choose GPU solver: DM, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs eng.grouping = 50; eng.probe_support_radius = []; eng.number_iterations = 50; eng.accelerated_gradients_start = inf; eng.mirror_objects = false; eng.share_object = false; [p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process eng.number_iterations = 50; eng.mirror_objects = true; eng.share_object = true; eng.share_probe = false; [p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process end run(fullfile( fileparts(mfilename('fullpath')), 'run_test.m')) % Academic License Agreement % % Source Code % % Introduction % • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR") % will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS % ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM"). % % Terms and Conditions of the LICENSE % 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 % hereinafter set out and until termination of this license as set forth below. % 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements % 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 % LICENSEE’s responsibility to ensure its proper use and the correctness of the results.” % 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 % A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. 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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 % another computing language: % "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 % Scherrer Institut, Switzerland." % % Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map: % P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008). % (doi: 10.1126/science.1158573), % for maximum likelihood: % P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012). % (doi: 10.1088/1367-2630/14/6/063004), % for mixed coherent modes: % P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806), % and/or for multislice: % 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). % (doi: 10.1364/OE.24.029089). % 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 % 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. % 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 % agrees to preserve same. 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