% PREPARE_FLYSCAN_POSITIONS from finit number of measured position interpolate possitions for each
% measured frame when fly scan is used
% 
% self = prepare_flyscan_positions(self, par)
% 
% 
% ** self      structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
% ** par       structure containing parameters for the engines 
%
% returns: 
% ++ self      structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..

% 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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%       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 mixed coherent modes:
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
% for LSQ-ML method 
% M. Odstrcil, A. Menzel, M.G. Sicairos,  Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
% for OPRP method 
%  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." Optics express 24.8 (2016): 8360-8369
% 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). 
% 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. 
% 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. 


function self = prepare_flyscan_positions(self, par)
import engines.GPU.GPU_wrapper.*
import math.*
import utils.*
import plotting.*


    jumps = diff(self.probe_positions_0);
    step = median(jumps,1);
    jumps = sum(abs(jumps),2);
    % empirical condition 
    jumps = find(jumps > 10*median(jumps));
    
  %% ADVANCED FLY SCAN - LINE SCAN 
    % interpolate the other modes into new positions 
    %pos = self.modes{1}.probe_positions;

    pos = self.probe_positions_0; %% modified by YJ, use initial position
    %scatter(pos(:,1),pos(:,2),'.'); axis image
    %hold on
    for ll = 1:par.Nmodes            
        ratio = par.flyscan_dutycycle*(ll-1)/par.Nmodes;
        self.modes{ll}.probe_positions = pos(min((1:self.Npos)+1,self.Npos),:)*ratio + (1-ratio)*pos;
        %disp(ll)
        %scatter(self.modes{ll}.probe_positions(:,1),self.modes{ll}.probe_positions(:,2),'.'); axis image
        if ~isempty(jumps)
            % expected step continuation
            self.modes{ll}.probe_positions(jumps,:) = bsxfun(@plus, self.modes{ll}.probe_positions(jumps-1,:),step);
        end         
    end

    %% PSI code
    %{
    if length(jumps) < par.Nscans
        % assume that smooth path is used 
       %% ADVANCED FLY SCAN - SPIRAL
        for ii = 1:par.Nscans
            assert(~any(isfinite(par.probe_position_search)), 'Position refinement and fly scans not suported')

            ind =  self.reconstruct_ind{ii};
            pos = self.probe_positions_0(ind,:);
            [ang, rad] = cart2pol(pos(:,1)-pos(1,1), pos(:,2)-pos(1,2)); 
            ang = unwrap(ang); 
            % get interpolate d positions of the sub probes 
            ang_all = ang + (par.flyscan_offset -0.5+linspace(0,par.flyscan_dutycycle*(par.Nmodes-1)/par.Nmodes, par.Nmodes)   ).*[diff(ang);0]; 
            rad_all = interp1(ang, rad, ang_all, 'pchip'); 
            [X,Y] = pol2cart(ang_all, rad_all);
            for ll = 1:par.Nmodes            
                    self.modes{ll}.probe_positions(ind,:) = pos(1,1:2) + [X(:,ll), Y(:,ll)];
                %if iter == 1;  self.probe{ll} = self.probe{1}; end
                %%deleted by YJ. seems a bug
            end
        end
    else
        %% ADVANCED FLY SCAN - LINE SCAN 
        % interpolate the other modes into new positions 
        pos = self.modes{1}.probe_positions;
        for ll = 1:par.Nmodes            
            ratio = par.flyscan_dutycycle*(ll-1)/par.Nmodes;
            self.modes{ll}.probe_positions = pos(min((1:self.Npos)+1,self.Npos),:)*ratio + (1-ratio)*pos;
            if ~isempty(jumps)
                % expected step continuation
                self.modes{ll}.probe_positions(jumps,:) = bsxfun(@plus, self.modes{ll}.probe_positions(jumps-1,:),step);
            end         
        end
    end
    %}
end