% template for artificial data generation for tests of multilayer
% reconstructions 

ptycho_path = fileparts(mfilename('fullpath')); 
ptycho_path = replace(ptycho_path, 'tests', ''); 
run(fullfile( ptycho_path, 'template_artificial_data.m'))

p.z = 0.7;  %  [m] sample to camera distance 
p.simulation.photons_per_pixel = inf;                             % Photon count; if photons_per_pixel = inf -> no noise 

p.simulation.energy = 6.2;                                     % Simulated energy
p.simulation.delta = [];                                        % Simulated refractive index (n = 1-delta+1j*beta); leave empty for CXRO values
p.simulation.beta = [];                                          % Simulated refractive index (n = 1-delta+1j*beta); leave empty for CXRO values
p.simulation.material_density = [-1];
% p.simulation.material = {'Al2O3'};                                     % Simulated material
% p.simulation.ref_index  = 1-1.2061e-05; % - 2.5742e-07i; 
p.simulation.dataset = {'3D_phantom'};                       % Simulated sample; see +core/+simulations/create_object for more information
p.simulation.rotation_angle = [];                            % apply rotation angle [degrees] on the 3D phantom  dataset, [] == ignore
p.simulation.flip_objects_180deg = [];                         % Simulated 0 vs 180 deg projection 
p.simulation.objheight = 5e-6;                                    % Object height of the simulated sample
p.simulation.apply_sub_px_shifts = false;                          % Allow sub-pixel shifts

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
p.simulation.thickness = 200e-6;  %%%  set effective thickness used for multilayer propagation, 0 == no propagation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

p.scan.   ly = 1e-6;                                                 % round_roi scan: width of the roi
p.scan.   lx = 3.5e-6;                                                 % round_roi scan: height of the roi
p.scan.   step = 0.2e-6;                                                % fermat: step size  

% p.simulation.material = {'Al2O3'};                                     % Simulated material
p.simulation.ref_index = 1  -2.1372e-05 - 4.0946e-07i;   % Al2O3 - loading from database for each angle is too slow 


% 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 
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%       OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4.	LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively, 
%       "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same 
%       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 
%       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 
%       in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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 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. 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.