%% 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.   verbose_level = -1;                             % level -1 -> keep it totally quiet
p.   artificial_data_file = 'tests/test_data_low_coherence.m';     % artificial data parameters 
p.   asize = [128 128];                              % size of the reconstruction probe 
p.   z = 5;                                          % distance sample to detector in meters

% Modes
p.   probe_modes  = 4;                                      % Number of coherent modes for probe
p.   object_modes = 1;                                      % Number of coherent modes for object
% Mode starting guess
p.   mode_start_pow = [0.02];                               % Normalized intensity on probe modes > 1. Can be a number (all higher modes equal) or a vector
p.   mode_start = 'herm';                                   % (for probe) = 'rand', = 'herm' (Hermitian-like base), = 'hermver' (vertical modes only), = 'hermhor' (horizontal modes only)
p.   ortho_probes = true;                                   % orthogonalize probes after each engine


% p.  use_display = false; 


%% ENGINES

if isunix
    % Please notice that you have to force data preparation (force_prepare_h5_files=true) if you have made any changes to 
    % the already prepared data (fmag, fmask, positions, sharing ...). 
    eng = struct();
    eng.  name = 'c_solver';
    eng.  method = 'DM+ML';
    eng.  number_iterations = 20;              % Total number of iterations
    eng.  opt_iter = 10;                       % Iterations for optimization     
    eng.  probe_regularization = .1;            % Weigth factor for the probe update; 
    eng.  probe_change_start = 1;               % Start updating probe at this iteration number
    eng.  probe_support_radius = 0.8;           % Normalized radius of circular support, = 1 for radius touching the window    
    eng.  pfft_relaxation = .05;                % Relaxation in the Fourier domain projection, = 0  for full projection    
    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
    eng.  probe_support_fft = false;            % [PARTIALLY IMPLEMENTED (not fully optimized)] Apply probe support in Fourier space, ! uses model zoneplate settings to estimate support size 

    eng.  N_layer = 1;                          % Number of virtual object layers (slices)
    eng.  delta_z = 0e-6 * ones(1, eng.N_layer-1); % Separation between object slices 
    %eng.  ms_init_ob_fraction = [1 0];
    if eng.  N_layer>1
        p.sufix = [p.sufix '_N' num2str(eng. N_layer)];
        eng.  number_iterations = 0; % highly recommended
    end
    
    eng.  single_prec = true;                   % single or double precision
    eng.  threads = 20;                         % number of threads for OMP
    eng.  beamline_nodes = [];                  % beamline nodes for the MPI/OMP hybrid, e.g. ['x12sa-cn-2'; 'x12sa-cn-3'];
    eng.  ra_nodes = 0;                         % number of nodes on ra cluster for the MPI/OMP hybrid; set to 0 for current node
    eng.  caller_suffix = '';                   % suffix for the external reconstruction program
    eng.  reconstruction_program = '';          % specify external reconstruction program that overwrites previous settings, e.g. 'OMP_NUM_THREADS=20 ./ptycho_single_OMP';
    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.
    eng.  initial_conditions_path = '';         % path of the initial conditions file; default if empty (== prepare_data_path)
    eng.  initial_conditions_file = '';    		% Name of the initial conditions file, default if empty. Do not use ~ in the path
    eng.  measurements_file = '';				% Name of the measurements file, default if empty. Do not use ~ in the path
    eng.  solution_file = '';                   % Name of the solution file, default if empty. Do not use ~ in the path
    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. 
    [p, ~] = core.append_engine(p, eng);        % Adds this engine to the reconstruction process
end

if 1
    eng = struct();
    eng. name = 'DM';
    eng. method = 'matlab'; 
    eng. number_iterations = 20;               % 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!!!)
    eng. use_mex = [0,0,0]; 
    [p, ~] = core.append_engine(p, eng);    % Adds this engine to the reconstruction process
end

    
run(fullfile( ptycho_path, 'tests/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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%       "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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%       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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% 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 
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%       the courts of Zürich, Switzerland.
