repair_BIDS_1_0_2.m

 function BIDS = repair_BIDS_1_0_2(input_dir)
% 
% Repair datasets for BIDS format, i.e. add missing PPG and RESP files
% this is not required for BIDS conversions 1.0.2 or higher
%
% Required fields of make_BIDS:
%
% input_dir  -  location of the GE data, use absolute path
%
%               data must have passed consistency checks using
%               consistency.m in MICHA_TEST/FA_consistency
%               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/FORSCHUNGSAMBULANZ/autoscripts_BIDS'
%
% function call, e.g.: repair_BIDS('/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/FOK0084')
%
% structure BIDS
% input.dir     - directory with verified data
%           e.g. BIDS.input.dir = '/run/media/spectro/DATAPART1/MICHA_TEST/FOR0015'
% input.biomax  - biomax_out filename
%
% file history:
% created M. Czisch 29.5.2018
% to repair BecomeVersion 1.0.1

fprintf('\nRepair BIDS \n');

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

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

BIDS = check_BIOMAX(BIDS);


% check and prepare temporary BIDS directory structure

pathInfo = what(BIDS.input.dir);
current_dir = pathInfo.path;
tmp_str = strsplit(current_dir,'/');
BIDS.output.dir = [current_dir,'/',tmp_str{end},'_BIDS'];


% load and format biomax_out info

biomax = load(BIDS.input.biomax);

biomax_table = array2table(biomax,...
    'VariableNames',{'Ser','Log','EDF','PPG','Analyzer','Blood'},...
    'RowNames',{'Loc';'T1w';'Cal';'rest1';...
                'EPI1';'TET';'FLAIR';'Reward';...
                'DTI';'Pepolar';'nback';'Loc2';...
                'Cal2';'faces';'EPI2';'rest2';...
                'IST';'Loc3';'rest3'});
            
            
% read content of GE EXAM and SERIES files

BIDS = read_GE_BIDS(BIDS);


% do repair

repair_PPG_BIDS(BIDS, biomax_table);


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

clear all