% CREATE_FILE_QUEUE create directories and .dat files for a file queue
% only needed if OMNY/flOMNI is not available
% ** start          start scan number
% ** stop           stop scan number
% ** step           reconstruction bundle size
% 
% *optional*        given as name/value pair
% ** dirpath        path to the .dat files directory; default: '../reconstruction'
% ** prop           structure with parameters that need to be saved to the .dat file
% ** prop_name      structure name; default: 'p'
% ** spec           path to spec file; needed for check2detpos
% ** check2detpos   check detector positions to avoid repeated scans
% ** det_motor      detector motor; default 'dettrx'
% ** verbose        set verbose level; default 0
%
% EXAMPLE:
%   s.lockfile = false;
%   s.energy = 6.2015;
%   s.check_nextscan_started = 1;
%   
%   create_file_queue(646, 650, 2, 'prop', s)
%
%
%   create_file_queue(287, 2553, 2, 'prop', s, 'spec', '/das/work/p16/p16812/data/pilatus/e16403/', 'check2detpos', true, 'det_motor', 'dettrx')

% 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).
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% 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 create_file_queue(start, stop, step, varargin)
import utils.*

par = inputParser;
par.addParameter('dirpath', '../reconstruction', @ischar) 
par.addParameter('prop', [], @isstruct)
par.addParameter('prop_name', 'p', @ischar)
par.addParameter('spec', [], @ischar)
par.addParameter('check2detpos', false, @logical)
par.addParameter('det_motor', 'dettrx', @ischar)
par.addParameter('verbose', 0, @isnumeric)

par.parse(varargin{:})

var = par.Results;

% reduce verbose level
vbl = utils.verbose;
utils.verbose(var.verbose);

% prepare directories
if ~exist(fullfile(var.dirpath), 'dir')
    mkdir(fullfile(var.dirpath))
end
if ~exist(fullfile(var.dirpath, 'in_progress'), 'dir')
    mkdir(fullfile(var.dirpath, 'in_progress'))
    mkdir(fullfile(var.dirpath, 'done'))
    mkdir(fullfile(var.dirpath, 'failed'))
end

% filename pattern
fname_pattern = repmat('scan%05d_',1,step);
fname_pattern = [fname_pattern(1:end-1) '.dat'];
scan_number_pattern = repmat('%d ',1,step);
scan_number_pattern = scan_number_pattern(1:end-1);

% get value for p.detector.check_2_detpos
if var.check2detpos
    
    S = io.spec_read(var.spec, 'ScanNr', start);
    detpos1 = S.(var.det_motor);
    for ii=start+1:stop
        S = io.spec_read(var.spec, 'ScanNr', ii);
        if S.(var.det_motor)~=detpos1
            detpos2=S.(var.det_motor);
            break
        end
    end
    var.prop.detector.check_2_detpos = abs(detpos1-detpos2)/2+detpos2;
end


% if needed, prepare structure
if ~isempty(var.prop)
    prop_fnames = utils.struc2cell(var.prop);
else
    prop_fnames = [];
end

utils.verbose(0, 'Creating file queue.');

ii = start;
if utils.verbose < 2
    utils.progressbar(1, round((stop-start)/step))
end
while ii<=stop
    % check if detector positions are repeated
    if var.check2detpos
        detpos = [];
        kk= 1;
        for jj=ii:ii+step-1
            S = io.spec_read(var.spec, 'ScanNr', jj);
            detpos(kk) = S.(var.det_motor);
            kk = kk+1;
        end
        if all(detpos == detpos(1))
            utils.verbose(2,'Found repeated detector positions.')
            ii = ii+1;
            continue
        end
    end
    
    % write file            
    fname = sprintf(fname_pattern, ii:ii+step-1);
    fid = fopen(fullfile(var.dirpath, fname), 'w');
    fprintf(fid, ['p.scan_number \t ' scan_number_pattern '\n'], ii:ii+step-1);
    if ~isempty(prop_fnames)
        for jj=1:numel(prop_fnames)
            cval = eval(['var.prop.' prop_fnames{jj}]);
            if islogical(cval) || isnumeric(cval)
                %eval(['var.prop.' prop_fnames{jj} '= double(var.prop.' prop_fnames{jj} ')']);
                prop_val = num2str(cval);
            else
                prop_val = cval;
            end
            prop_val = replace(prop_val, '%', '%%');   % avoid interpretation of special characters in strings 
            fprintf(fid, [var.prop_name '.' prop_fnames{jj} '\t ' prop_val '\n']);
        end
    end
    
    fclose(fid);    
    
    ii = ii+step;
    if utils.verbose < 2
        utils.progressbar(ii-start, round((stop-start)/step))
    end
end

utils.verbose(0, '\nDone.');

% revert changes to verbose level
utils.verbose(vbl);

end