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162 lines
12 KiB
Matlab
162 lines
12 KiB
Matlab
%% TEST TEMPLATE FOR FUNTIONALITY CHECK OF MULTILAYER EXTENSION 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 DETERIORATION STILL NEED TO BE MEASURED !!
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%% set shared parameters for all test scripts
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run(fullfile( fileparts(mfilename('test_ML_data')), 'init_test.m'))
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%% general settings
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p. artificial_data_file = 'tests/test_ML_data.m'; % artificial data parameters
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p. asize = [192 192]; % size of the reconstruction probe
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%% load simulation parameters
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run(fullfile( ptycho_path, p.artificial_data_file))
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Nlayers = length(p.simulation.dataset{1});
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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. keep_on_gpu = true; % keep data + projections on GPU, false is useful for large data if DM is used
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eng. compress_data = true; % use automatic online memory compression to limit meed of GPU memory
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eng. gpu_id = []; % default GPU id, [] means choosen by matlab
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eng. check_gpu_load = true; % check available GPU memory before starting GPU engines
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%% general
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% eng. number_iterations = 50; % number of iterations for selected method
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%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.
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%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.
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% eng. method = 'MLs'; % choose GPU solver: DM, RAAR, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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eng. opt_errmetric = 'L1' ; % optimization likelihood - poisson, L1
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eng. grouping = 50; % 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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% for pPIE, MLc the convergence is similar
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% for DM, RAAR is has no effect on convergence
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%eng. probe_modes = 1; % Number of coherent modes for probe
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eng. object_change_start = 1; % Start updating object at this iteration number
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eng. probe_change_start = 1; % Start updating probe at this iteration number
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% regularizations
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eng. reg_mu = 0; % Regularization constant ( = 0 for no regularization)
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eng. background = 1e-3;
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eng. delta = 0; % press values to zero out of the illumination area, usually 1e-2 is enough
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eng. positivity_constraint_object = 0; % enforce weak positivity in object, usually 1e-2 is already enough
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eng. regularize_layers = 0.01; % 0<R<<1 -> apply regularization on the reconstructed object layers, 0 == no regularization
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eng. apply_multimodal_update = false; % apply all incoherent modes to object, it can cause isses if the modes collect some crap
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eng. probe_backpropagate = 0; % backpropagate the probe mask, inf == farfield
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% basic recontruction parameters
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% PIE / ML methods
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eng. beta_object = 1; % object step size, larger == faster convergence, smaller == more robust, should not exceed 1
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eng. beta_probe = 1; % probe step size, larger == faster convergence, smaller == more robust, should not exceed 1
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eng. delta_p = 0.1; % LSQ dumping constant, 0 == no preconditioner, 0.1 is usually safe,
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% DM
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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;% Weigth factor for the probe update (inertia)
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% ADVANCED OPTIONS
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% position refinement
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eng. apply_subpix_shift = false; % apply FFT-based subpixel shift, important for good position refinement but it is slow
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eng. probe_position_search = inf; % reconstruct probe positions, from iteration == probe_position_search, assume they have to match geometry model with error less than probe_position_error_max
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eng. probe_position_error_max = 10e-9; % max expected random position error of the stages
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% wavefront refinement
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eng. probe_fourier_shift_search = inf; % refine farfield position of the beam (ie angle) from iteration == probe_fourier_shift_search
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eng. estimate_NF_distance = inf; % try to estimate the nearfield propagation distance
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eng. variable_probe = false; % Use SVD to account for variable illumination during a single (coupled) scan
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eng. variable_SVD_modes = 3; % OPRP settings , number of SVD modes, apply only for PIE methods
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eng. variable_probe_smooth = 0; % OPRP settings , apply assumption of smooth evolution of the OPRP modes (ie slow drifts)
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eng. variable_intensity = false; % account to changes in probe intensity
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eng_0 = eng;
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if 1
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%% test multilayer extension
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eng = eng_0;
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eng.delta_z = p.simulation.thickness / (Nlayers-1) * ones(Nlayers-1,1);
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eng.mirror_objects = false;
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eng.share_object = false;
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eng.probe_support_radius = [];
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eng.get_fsc_score = false;
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%eng.plot.interval = 50;
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eng.number_iterations = 100; % number of iterations for selected method
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eng.grouping = 100; % number of iterations for selected method
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eng. method = 'MLc'; % choose GPU solver: DM, RAAR, ePIE, pPIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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eng.momentum = true;
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eng.regularize_layers = 0;
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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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