%% TEST TEMPLATE FOR FUNTIONALITY CHECK OF CPU 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'))

%% general settings
p.   artificial_data_file = 'tests/test_data.m';     % artificial data parameters 
p.   asize = [192 192];                              % size of the reconstruction probe 
p.   binning = 1;                                    % binning will be 2^p.binning
p.   z = 5;                                          % distance sample to detector in meters

%% ENGINES

eng = struct();
eng. name = 'DM';
eng.  method = 'DM'; 
eng. number_iterations = 5;               % Total number of iterations
eng. probe_change_start = 1;              % Start updating probe at this iteration number
eng. average_start = 300;                 % Start averaging at this iteration number
eng. average_interval = 5;                % Number of iterations between reconstruction estimates for average 
eng. count_bound = 4e-2;                  % Relaxed Fourier projection parameter - average photons of change per pixel (= 0 no relaxation) 
eng. pfft_relaxation = 0.05 ;               % Relaxation in the Fourier domain projection, = 0  for full projection 
eng. probe_regularization = .1;           % Weigth factor for the probe update
eng. probe_mask_bool = true;              % If true, impose a support constraint to the probe
eng. probe_mask_area = .9;                % Area ratio of the mask
eng. probe_mask_use_auto = false;         % Use autocorrelation for probe_mask (if false: circular circle)
eng. object_flat_region = [];             % Mask for enforcing a flat region in the object (to reduce artifacts)
eng. remove_scaling_ambiguity = true;     % Remove ambiguity of the probe times object scalling by probe normalization
eng. clip_object = true;                  % Clip the object transmission function
eng. clip_max = 1.0;                      % Upper bound
eng. clip_min = 0.0;                      % Lower bound
eng. compute_rfact = false;               % If set to true, R-factor is computed at every iteration (large overhead!!!)

[p, ~] = core.append_engine(p, eng);    % Adds this engine to the reconstruction process


    
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") 
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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 
%       another computing language:
%       "Data processing was carried out using the PtychoShelves 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 
% K. Wakonig, H.-C. Stadler, M. Odstrčil, E.H.R. Tsai, A. Diaz, M. Holler, I. Usov, J. Raabe, A. Menzel, M. Guizar-Sicairos, PtychoShelves, a versatile 
% high-level framework for high-performance analysis of ptychographic data, J. Appl. Cryst. 53(2) (2020). (doi: 10.1107/S1600576720001776)
% and 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 LSQ-ML:
% M. Odstrčil, A. Menzel, and M. Guizar-Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Opt. Express 26(3), 3108 (2018). 
%   (doi: 10.1364/OE.26.003108),
% 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),
% and/or for OPRP:
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby,  Ptychographic coherent diffractive imaging with orthogonal probe relaxation. 
% Opt. Express 24.8 (8360-8369) 2016. (doi: 10.1364/OE.24.008360).
% 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.
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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 
%       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: 
%       © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017. 
% 8.	The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9.	DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate 
%       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, 
%       in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software 
%       in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 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 
%       the courts of Zürich, Switzerland.
