%CREATE_OBJECT create object for artificial scans
% select object with p.simulation.dataset in your simulation template
% 
%  [obj,ref_index] = create_object(p)
%
% Inputs: 
%  ** p  - p-struct 
%  *Outputs*
% ++ obj - generate real-valued positive image 
% ++ ref_index   - refractive index of the simulated sample 


% 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").
%
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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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%       "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 
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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: 
%       © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017. 
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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, 
%       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. 

function [obj,ref_index] = create_object(p)
    import utils.crop_pad
    import utils.get_ref_index


%% get refractive index
if ~isfield(p.simulation, 'ref_index')
    for ii = 1:size(p.simulation.material,2)
        ref = get_ref_index(p.simulation.material{ii}, p.energy, p.simulation.material_density(ii));
        delta(ii) = ref(2);
        beta(ii) = ref(3);
    end
else
    delta = -real(p.simulation.ref_index-1); 
    beta = -imag(p.simulation.ref_index); 
end
ref_index = 1 - delta - 1i*beta; 

%% load object
img_path = fullfile(p.ptycho_matlab_path, 'utils', 'imgs');
for jj = 1:p.numscans
    Npix = p.object_size(min(jj,end),:);

    if isstr(p.simulation.dataset{jj})
        % apply rotation of provided
        if isfield(p, 'rotation_angle') && ~isempty(p.rotation_angle)
            rotate = p.rotation_angle(min(end,jj)); 
        elseif isfield(p.simulation, 'rotation_angle') && ~isempty(p.simulation.rotation_angle)
            rotate = p.simulation.rotation_angle(min(end,jj)); 
        else
            rotate = []; 
        end
        obj{jj}(:,:,1,:) = generate_virtual_object(p, p.simulation.dataset{jj},img_path, Npix , rotate); 
    else
        for ii = 1:length(p.simulation.dataset{jj})
            obj{jj}(:,:,1,ii) = generate_virtual_object(p, p.simulation.dataset{jj}(ii),img_path, Npix,[]); 
        end
    end
    obj{jj} = rot90(exp(1i*(2*pi/p.lambda)*(1i*beta-delta)*(1-obj{jj})*p.simulation.objheight / size(obj{jj},4)),2);
    
    % remove offset caused by positioning padding due to variable
    % object_size, if p.positions_pad == 0 , it will have no effect 
    % the missing values will be filled by fully transparent value 
    if any(p.positions_pad)
        obj{jj} = reshape(utils.imshift_fast(obj{jj}, p.positions_pad(1),p.positions_pad(2),[],'nearest',1), size(obj{jj})); 
    end
    
    % emulate 0 vs 180 deg scan 
    if ~isempty(p.simulation.flip_objects_180deg) && p.simulation.flip_objects_180deg(min(end,jj)) == true
        obj{jj} = fliplr(obj{jj}); 
        obj{jj} = obj{jj}(:,:,1,end:-1:1); 
    end
end


end