OPTIMA_make_BIDS_2.m

 function BIDS = OPTIMA_make_BIDS_2(input_dir)
% 
% Prepare datasets for BIDS format, version 2, created 1.7.2019
%
% Required fields of make_BIDS:
%
% input_dir  -  location of the GE data, use absolute path
%
%               data must have passed consistency checks using
%               OPTIMA_consistency.m in /run/media/spectro/DATAPART1/OPTIMA/autoscripts_BIOMAX
%               the script is expecting a file named
%               "biomax_out_*_VERIFIED*.txt" or
%               "biomax_out_*_MODIFIED*.txt" 
%               to be present in the subjects main directory
% 
% directories must be known:
% addpath '/run/media/spectro/DATAPART1/OPTIMA/autoscripts_BIDS'
%
% function call, e.g.: OPTIMA_make_BIDS_2('/run/media/spectro/DATAPART1/OPTIMA/PTP0270_T0')
%
% structure BIDS
% input.dir     - directory with verified data
%           e.g. BIDS.input.dir = '/run/media/spectro/DATAPART1/OPTIMA/PTP0270_T0'
% input.biomax  - biomax_out filename
%
% file history:
% created M. Czisch 1.7.2019
% last modified 12.9.2019 M. Czisch to include SIT1
% BecomeVersion 1.0.2

fprintf('\n\nStart BIDS conversion\n');

clear BIDS
BIDS.input.dir = input_dir;
BIDS.output.dir = '';
BIDS.autoscripts.dir = '/run/media/spectro/DATAPART1/OPTIMA/autoscripts_BIDS';


% have the data being for consistency checked already?
% does biomax_out exist?

BIDS = OPTIMA_check_BIOMAX(BIDS);


% check and prepare temporary BIDS directory structure

pathInfo = what(BIDS.input.dir);
current_dir = pathInfo.path;

BIDS.output.dir = [current_dir,'/BIDS/'];

OPTIMA_check_BIDS(BIDS.input.dir); %OK
mkdir_BIDS(BIDS.output.dir); %OK



% load and format biomax_out info

biomax = load(BIDS.input.biomax);

biomax_table = array2table(biomax,...
    'VariableNames',{'Ser','Log','EDF','PPG'},...
    'RowNames',{'Loc';'T1w';'Cal';'rest1';...
                'EPI1';'FLAIR';'SIT1';...
                'DTI';'Pepolar'});
            
% copy biomax_out file to BIDS directory

cmd_str = sprintf('cp %s %s/%s', BIDS.input.biomax, BIDS.output.dir, BIDS.input.biomax); system(cmd_str);

              
            
% read content of GE EXAM and SERIES files

BIDS = OPTIMA_read_GE_BIDS(BIDS);


% do the conversion to BIDS format

OPTIMA_convert_GE_BIDS_2(BIDS, biomax_table);


% make a json file with dataset description

OPTIMA_dataset_description_BIDS(BIDS,biomax_table);                   
            

% copy the ANALYZER files to BIDS naming format
% does not apply for OPTIMA, this is from BeCOME
% OPTIMA_convert_ANALYZER_BIDS_2(BIDS,biomax_table);


% do the conversion of logfiles to BIDS naming format

OPTIMA_convert_LOG_BIDS_2(BIDS,biomax_table);

% do the conversion of EDF files to BIDS naming format

OPTIMA_convert_EDF_BIDS_2(BIDS,biomax_table);

% do the conversion of PPG and RESP files to BIDS 

OPTIMA_convert_PPG_BIDS_2(BIDS, biomax_table);


% do tsv conversion of logfiles

%Hariri_logfile_bids(BIDS,biomax_table);
%NBack_logfile_bids(BIDS,biomax_table);
%TET_logfile_bids(BIDS,biomax_table);



cd([BIDS.input.dir]);

% finally, rename the BIDS directory to a proper name

cmd_str = ['rm -r ', BIDS.output.dir,'../',BIDS.input.data_dir(1).PatientID{3},'_BIDS'];
system(cmd_str);

cmd_str = ['mv ', BIDS.output.dir,' ', BIDS.output.dir,'../',BIDS.input.data_dir(1).PatientID{3},'_BIDS'];
system(cmd_str);

fprintf('\n\ndone %s\n', BIDS.input.data_dir(1).PatientID{3});

clear all