dataset_description_BIDS2.m

function dataset_description_BIDS(BIDS,biomax_table)
% 
% create BIDS dataset description json file
%  
%
% file history:
% created M. Czisch 13.2.2018

clear jsonstruct;

% read general info from master file

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

fname = [BIDS.autoscripts.dir,'/masterfile.json']; 
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, short_ID],'"'];
fprintf(fid2, '    %s\n', str);

% biomax -> json
% cave: a minus sign is not allowed in the json name
% therefore, e.g. "rest_run-1" needs to be replaced by "rest_run_1"

% jsonstruct.Loc                  = jsonencode(biomax_table(1,:));
% jsonstruct.T1w                  = jsonencode(biomax_table(2,:));
% jsonstruct.Cal                  = jsonencode(biomax_table(3,:));
% jsonstruct.rest_run_1           = jsonencode(biomax_table(4,:));
% jsonstruct.inplaneT2star_run_1  = jsonencode(biomax_table(5,:));
% jsonstruct.tet                  = jsonencode(biomax_table(6,:));
% jsonstruct.FLAIR                = jsonencode(biomax_table(7,:));
% jsonstruct.reward               = jsonencode(biomax_table(8,:));
% jsonstruct.run_1_dwi            = jsonencode(biomax_table(9,:)); 
% jsonstruct.run_2_dwi            = jsonencode(biomax_table(10,:));
% jsonstruct.nback                = jsonencode(biomax_table(11,:));
% jsonstruct.Loc2                 = jsonencode(biomax_table(12,:));
% jsonstruct.Cal2                 = jsonencode(biomax_table(13,:));
% jsonstruct.hariri               = jsonencode(biomax_table(14,:));   
% jsonstruct.inplaneT2star_run_2  = jsonencode(biomax_table(15,:));
% jsonstruct.rest_run_2           = jsonencode(biomax_table(16,:));
% jsonstruct.ist                  = jsonencode(biomax_table(17,:));
% jsonstruct.Loc3                 = jsonencode(biomax_table(18,:));
% jsonstruct.rest_run_3           = jsonencode(biomax_table(19,:));

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