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%% TEST TEMPLATE FOR FUNTIONALITY CHECK OF CPU 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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close all
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plot_results = true;
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plot_save_results = true;
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%% general settings
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p. artificial_data_file = 'tests/test_data_double_scan.m'; % artificial data parameters
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p. asize = [128 128]; % size of the reconstruction probe
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Nlayers = 2;
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%% Plot, save and analyze
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p. plot.prepared_data = false; % plot prepared data
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p. plot.interval = []; % plot each interval-th iteration, does not work for c_solver code
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p. plot.log_scale = [1 1]; % Plot on log scale for x and y
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p. plot.realaxes = true; % Plots show scale in microns
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p. plot.remove_phase_ramp = true; % Remove phase ramp from the plotted / saved phase figures
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p. plot.fov_box = true; % Plot the scanning FOV box on the object (both phase and amplitude)
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p. plot.fov_box_color = 'r'; % Color of the scanning FOV box
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p. plot.positions = true; % Plot the scanning positions
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p. plot.mask_bool = true; % Mask the noisy contour of the reconstructed object in plots
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p. plot.windowautopos = true; % First plotting will auto position windows
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p. plot.obj_apod = false; % Apply apodization to the reconstructed object;
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p. plot.prop_obj = 1e-12; % Distance to propagate reconstructed object before plotting [m]
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p. plot.show_layers = true; % show each layer in multilayer reconstruction
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p. plot.show_layers_stack = true; % show each layer in multilayer reconstruction by imagesc3D
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p. plot.object_spectrum = true; % Plot propagated object (FFT for conventional ptycho); if empty then default is false if verbose_level < 3 and true otherwise
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p. plot.conjugate = true; % plot complex conjugate of the reconstruction
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p. plot.horz_fact = 2.5; % Scales the space that the ptycho figures take horizontally
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p. plot.FP_maskdim = 180e-6; % Filter the backpropagation (Fourier Ptychography)
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p. plot.calc_FSC = true; % Calculate the Fourier Shell correlation for 2 scans or compare with model in case of artificial data tests
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p. plot.show_FSC = true; % Show the FSC plots, including the cropped FOV
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p. plot.residua = true; % highlight phase-residua in the image of the reconstructed phase
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%% ENGINES
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if isunix
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% Please notice that you have to force data preparation (force_prepare_h5_files=true) if you have made any changes to
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% the already prepared data (fmag, fmask, positions, sharing ...).
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eng. name = 'c_solver';
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eng. method = 'DM+ML';
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eng. number_iterations = 100; % Total number of iterations
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eng. opt_iter = 100; % Iterations for optimization
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eng. probe_regularization = .1; % Weigth factor for the probe update;
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eng. probe_change_start = 1; % Start updating probe at this iteration number
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eng. probe_support_radius = 0.8; % Normalized radius of circular support, = 1 for radius touching the window
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eng. pfft_relaxation = .05; % Relaxation in the Fourier domain projection, = 0 for full projection
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eng. background = 0; % [PARTIALLY IMPLEMENTED (not fully optimized)] Add background to the ML model in form: |Psi|^2+B, B is in average counts per frame and pixel
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eng. probe_support_fft = false; % [PARTIALLY IMPLEMENTED (not fully optimized)] Apply probe support in Fourier space, ! uses model zoneplate settings to estimate support size
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eng. N_layer = Nlayers; % Number of virtual object layers (slices)
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eng. delta_z = 10e-6 * ones(1, eng.N_layer-1); % Separation between object slices
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%eng. ms_init_ob_fraction = [1 0];
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if eng. N_layer>1
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p.suffix = [p.suffix '_N' num2str(eng. N_layer)];
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eng. number_iterations = 0; % highly recommended
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end
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eng. single_prec = true; % single or double precision
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eng. threads = 20; % number of threads for OMP
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eng. beamline_nodes = []; % beamline nodes for the MPI/OMP hybrid, e.g. ['x12sa-cn-2'; 'x12sa-cn-3'];
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eng. ra_nodes = 0; % number of nodes on ra cluster for the MPI/OMP hybrid; set to 0 for current node
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eng. caller_suffix = ''; % suffix for the external reconstruction program
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eng. reconstruction_program = ''; % specify external reconstruction program that overwrites previous settings, e.g. 'OMP_NUM_THREADS=20 ./ptycho_single_OMP';
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eng. check_cpu_load = true; % check if specified nodes are already in use (only x12sa). Disable check if you are sure that the nodes are free.
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eng. initial_conditions_path = ''; % path of the initial conditions file; default if empty (== prepare_data_path)
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eng. initial_conditions_file = ''; % Name of the initial conditions file, default if empty. Do not use ~ in the path
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eng. measurements_file = ''; % Name of the measurements file, default if empty. Do not use ~ in the path
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eng. solution_file = ''; % Name of the solution file, default if empty. Do not use ~ in the path
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eng. force_prepare_h5_files = 1; % If true before running the C-code the data h5 file is created and the h5 file with initial object and probe too, regardless of whether it exists. It will use the matlab data preparator.
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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else
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eng = struct();
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eng. name = 'DM';
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eng. method = 'matlab';
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eng. number_iterations = 10; % Total number of iterations
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eng. probe_change_start = 1; % Start updating probe at this iteration number
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eng. average_start = 300; % Start averaging at this iteration number
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eng. average_interval = 5; % Number of iterations between reconstruction estimates for average
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eng. count_bound = 4e-2; % Relaxed Fourier projection parameter - average photons of change per pixel (= 0 no relaxation)
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eng. pfft_relaxation = 0.05 ; % Relaxation in the Fourier domain projection, = 0 for full projection
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eng. probe_regularization = .1; % Weigth factor for the probe update
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eng. probe_mask_bool = true; % If true, impose a support constraint to the probe
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eng. probe_mask_area = .9; % Area ratio of the mask
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eng. probe_mask_use_auto = false; % Use autocorrelation for probe_mask (if false: circular circle)
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eng. object_flat_region = []; % Mask for enforcing a flat region in the object (to reduce artifacts)
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eng. remove_scaling_ambiguity = true; % Remove ambiguity of the probe times object scalling by probe normalization
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eng. clip_object = true; % Clip the object transmission function
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eng. clip_max = 1.0; % Upper bound
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eng. clip_min = 0.0; % Lower bound
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eng. compute_rfact = false; % If set to true, R-factor is computed at every iteration (large overhead!!!)
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eng. use_mex = [0,0,0];
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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( ptycho_path, 'tests/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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