OPTIMA_dataset_func_description_BIDS_5.m

function OPTIMA_dataset_func_description_BIDS_5(BIDS,fname_in,biomax_vec)
% 
% create BIDS dataset description json file
% for the functional data  
%
% file history:
% created M. Czisch 19.2.2018
% last modified 13.11.2019

clear jsonstruct;

% read general info from master file

fname_out = [BIDS.output.dir,'tmp.json'];
cmd_str = ['rm -rf ', fname_out]; system(cmd_str);
fid2 = fopen(fname_out,'a');

%fname = [BIDS.autoscripts.dir,'/masterfile_1_0_2.json']; 

fname = fname_in;
fid = fopen(fname); 
last_line = fgetl(fid);

while ~strcmp(last_line,'}')
    if strcmp(last_line,'{')
        second_to_last_line = last_line;
        last_line = fgetl(fid);
    else
        fprintf(fid2, '%s\n', second_to_last_line);
        second_to_last_line = last_line;
        last_line = fgetl(fid);
    end
end
fprintf(fid2, '%s,\n', second_to_last_line);

% add specific info for current dataset
str = ['"TimeOfConversion": "',char(date),'"'];
fprintf(fid2, '        %s,\n', str);

short_ID = data_set_short_ID(BIDS);

str = ['"PatientID": "',[BIDS.output.dir],'"']; fprintf(fid2, '        %s,\n', str);
str = ['"NumberShots": 1']; fprintf(fid2, '        %s,\n', str);
str = ['"ParallelAcquisitionTechnique": "ASSET"']; fprintf(fid2, '        %s,\n', str);
str = ['"ParallelReductionFactorInPlane": 2']; fprintf(fid2, '        %s,\n', str);
str = ['"PhaseEncodingDirection": "j"']; fprintf(fid2, '        %s,\n', str);
str = ['"SliceEncodingDirection": "k"']; fprintf(fid2, '        %s,\n', str);
str = ['"NumberOfVolumesDiscardedByScanner": 0']; fprintf(fid2, '        %s,\n', str);
str = ['"NumberOfVolumesDiscardedByUser": 0']; fprintf(fid2, '        %s,\n', str);

% if logical(strfind(fname,'task-ist_bold'))
%     str = ['"NumberSlices": 40']; fprintf(fid2, '        %s,\n', str);
%     str = ['"SliceTiming": [0.00, 1.00, 0.05, 1.05, 0.10, 1.10, 0.15, 1.15, 0.20, 1.20,'...
%                            '0.25, 1.25, 0.30, 1.30, 0.35, 1.35, 0.40, 1.40, 0.45, 1.45,'...
%                            '0.50, 1.50, 0.55, 1.55, 0.60, 1.60, 0.65, 1.65, 0.70, 1.70,'...
%                            '0.75, 1.75, 0.80, 1.80, 0.85, 1.85, 0.90, 1.90, 0.95, 1.95]']; fprintf(fid2, '    %s,\n', str);
% else
%     str = ['"NumberSlices": 42']; fprintf(fid2, '        %s,\n', str);
%     str = ['"SliceTiming": [0, 1.2500, 0.0595, 1.3095, 0.1190, 1.3690, 0.1786, 1.4286,'...
%                            '0.2381, 1.4881, 0.2976, 1.5476, 0.3571, 1.6071, 0.4167, 1.6667,'...
%                            '0.4762, 1.7262, 0.5357, 1.7857, 0.5952, 1.8452, 0.6548, 1.9048,'...
%                            '0.7143, 1.9643, 0.7738, 2.0238, 0.8333, 2.0833, 0.8929, 2.1429,'...
%                            '0.9524, 2.2024, 1.0119, 2.2619, 1.0714, 2.3214, 1.1310, 2.3810, 1.1905, 2.4405]']; 
%                            fprintf(fid2, '        %s,\n', str);    
% end

str = sprintf('"MRIDataExist": %d', biomax_vec(1)); fprintf(fid2, '        %s,\n', str);
str = sprintf('"LogFileExist": %d', biomax_vec(2)); fprintf(fid2, '        %s,\n', str);
str = sprintf('"EyeTrackerExist": %d', biomax_vec(3)); fprintf(fid2, '        %s,\n', str);
str = sprintf('"PhysioDay1Exist": %d', biomax_vec(4)); fprintf(fid2, '        %s,\n', str);
%str = sprintf('"PhysioDay2Exist": %d', biomax_vec(5)); fprintf(fid2, '        %s\n', str);

str = '}';
fprintf(fid2, '%s', str);
fclose(fid); fclose(fid2); 

cmd_str = sprintf('mv %s %s', fname_out, fname); system(cmd_str);