eegmp_preproc/code/a6_automatic_artifact_correction/H_STSW_automatic_artifact_correction_180123.m

function H_STSW_automatic_artifact_correction_180123(id)

%% H_SS_automatic_artifact_correction_20170922

%% initialize

%restoredefaultpath;
%clear all; close all; pack; clc;

%% pathdef

if ismac
%     pn.study        = '/Volumes/LNDG/Projects/StateSwitch/';
%     pn.eeg_root     = [pn.study, 'dynamic/data/eeg/task/A_preproc/SA_preproc_study_YA/'];
    pn.eeg_root     = '/Users/kosciessa/Desktop/mountpoint_tardis_LNDG/LNDG/StateSwitch/WIP_eeg/SA_preproc_study_YA/';
    pn.dynamic_In   = [pn.eeg_root, 'B_data/B_EEG_ET_ByRun/'];
    pn.triggerTiming= [pn.eeg_root, 'C_figures/D_TriggerTiming/'];
    pn.EEG          = [pn.eeg_root, 'B_data/C_EEG_FT/']; mkdir(pn.EEG);
    pn.History      = [pn.eeg_root, 'B_data/D_History/']; mkdir(pn.History);
    pn.logs         = [pn.eeg_root, 'Y_logs/H_ArtCorr/'];
    % add ConMemEEG tools
    pn.MWBtools     = [pn.eeg_root, 'T_tools/fnct_MWB/'];           addpath(genpath(pn.MWBtools));
    pn.THGtools     = [pn.eeg_root, 'T_tools/fnct_THG/'];           addpath(genpath(pn.THGtools));
    pn.commontools  = [pn.eeg_root, 'T_tools/fnct_common/'];        addpath(genpath(pn.commontools));
    pn.fnct_JQK     = [pn.eeg_root, 'T_tools/fnct_JQK/'];           addpath(genpath(pn.fnct_JQK));
    pn.FT           = [pn.eeg_root, 'T_tools/fieldtrip-20170904/']; addpath(pn.FT); ft_defaults;
    pn.helper       = [pn.eeg_root, 'A_scripts/helper/'];           addpath(pn.helper);
else
    pn.root         = '/home/mpib/LNDG/StateSwitch/WIP_eeg/SA_preproc_study_YA/';
    pn.EEG          = [pn.root, 'B_data/C_EEG_FT/'];
    pn.History      = [pn.root, 'B_data/D_History/'];
    pn.triggerTiming= [pn.root, 'C_figures/D_TriggerTiming/'];
    pn.logs         = [pn.root, 'Y_logs/H_ArtCorr/'];
end

%% define Condition & IDs for preprocessing

condEEG = 'dynamic';

%% define IDs for segmentation

% N = 47;
IDs = {'1117';'1118';'1120';'1124';'1126';'1131';'1132';'1135';'1136';'1138';'1144';'1151';'1158';'1160';'1163';'1164';'1167';'1169';'1172';'1173';'1178';'1182';'1215';'1216';'1219';'1221';'1223';'1227';'1228';'1233';'1234';'1237';'1239';'1240';'1243';'1245';'1247';'1250';'1252';'1257';'1261';'1265';'1266';'1268';'1270';'1276';'1281'};

id = str2num(id);

%%  loop IDs

ID_unavailable = cell(length(IDs),1);
%for id = 1:length(IDs)
    try
        display(['processing ID ' num2str(IDs{id})]);
        for iRun = 1:4
        
            % load data
            load([pn.EEG, IDs{id}, '_r',num2str(iRun), '_', condEEG, '_EEG_Rlm_Fhl_rdSeg'],'data_EEG');
            
            dataICA = load([pn.EEG, IDs{id}, '_', condEEG, '_EEG_Rlm_Fhl_Ica'],'data');

            data = data_EEG; clear data_EEG;
            data.elec = dataICA.data.elec;
            data.chanlocs = dataICA.data.chanlocs; clear dataICA;
            
           %% ------------------ ARTIFACT DETECTION - PREPARATION ----------------- %%

            % load config

            load([pn.History, IDs{id}, '_r',num2str(iRun), '_', condEEG, '_config'],'config')
            
            config.elec = data.elec;

            %% ICA (from weights)

            % ica config
            cfg.method           = 'runica';
            cfg.channel          = {'all','-ECG','-A2'};
            cfg.trials           = 'all';
            cfg.numcomponent     = 'all';
            cfg.demean           = 'yes';
            cfg.runica.extended  = 1;

            % ICA solution
            cfg.unmixing     = config.ica1.unmixing;
            cfg.topolabel    = config.ica1.topolabel;

            % components
            comp = ft_componentanalysis(cfg,data);

            % clear cfg
            clear cfg data

            %% remove components

            % get IC labels
            iclabels = config.ica1.iclabels.manual;

            % cfg for rejecting components (reject: blinks, eye movements,
            % ecg, ref); JQK: added artifacts and emg
            cfg.component = sortrows([iclabels.bli(:); iclabels.mov(:); iclabels.hrt(:); iclabels.ref(:); iclabels.art(:); iclabels.emg(:)])';
            cfg.demean    = 'yes';

            % reject components
            data = ft_rejectcomponent(cfg,comp);

            % clear cfg
            clear cfg comp

            %% remove eye & reference channels

            cfg.channel     = {'all','-IOR','-LHEOG','-RHEOG','-A1'};
            cfg.demean      = 'yes';

            % remove channels
            tmpdat = ft_preprocessing(cfg,data);

            % clear cfg & data variable
            clear cfg data


            %% ------------------------- ARTIFACT DETECTION ------------------------ %%

            % open log file
            fid = fopen([pn.logs, 'log_' IDs{id}, '_r',num2str(iRun), '_' condEEG '_ArtCorr.txt'],'a');

            % write log
          % fprintf(fid,['*********************  ' BLOCK '  *********************\n']);                         % Undefined function or variable 'BLOCK'. but see: %% H_prep_data_for_analysis_20141218

            fprintf(fid,['*********************   BLOCK   *********************\n']);
            fprintf(fid,['function: H_SS_automatic_artifact_correction_20170922.m \n\n']);                
            fprintf(fid,['eeg file = ' config.data_file '\n\n']);

            n_trl = length(tmpdat.trial);

            %%  get artifact contaminated channels by kurtosis, low & high frequency artifacts

            cfg.criterion = 3;
            cfg.recursive = 'no';

            [index0 parm0 zval0] = cm_MWB_channel_x_epoch_artifacts_20170922(cfg,tmpdat);

            % write log
            tmp_log = '';
            for j = 1:length(index0.c)
                tmp_log = [tmp_log num2str(index0.c(j)) ' '];
            end; clear j
            tmp_log = [tmp_log(1:end-1) '\n'];
            fprintf(fid,'(1) automatic bad channel detection:\n');
            fprintf(fid,['MWB:          channel(s) ' tmp_log]);

            % clear cfg
            clear cfg tmp_log

            %%  get artifact contaminated channels by FASTER

            cfg.criterion = 3;
            cfg.recursive = 'no';

            [index1 parm1 zval1] = THG_FASTER_1_channel_artifacts_20140302(cfg,tmpdat);

            % write log
            tmp_log = '';
            for j = 1:length(index1)
                tmp_log = [tmp_log num2str(index1(j)) ' '];
            end; clear j
            tmp_log = [tmp_log(1:end-1) '\n'];
            fprintf(fid,['FASTER:      channel(s) ' tmp_log]);

            % clear cfg
            clear cfg tmp_log

            %%  interpolate artifact contaminated channels

            % collect bad channels
            badchan = unique([index0.c; index1]);

            fprintf(fid,['--> ' num2str(length(badchan)) ' channels interpolated\n\n']);
            
            cfg.method     = 'spline';
            cfg.badchannel = tmpdat.label(badchan);
            cfg.trials     = 'all';
            cfg.lambda     = 1e-5; 
            cfg.order      = 4; 
            cfg.elec       = config.elec;

            % interpolate
            tmpdat = ft_channelrepair(cfg,tmpdat);

            % clear cfg
            clear cfg

            %% equalize duration of trials to the trial with fewest samples
            
            for indTrial = 1:64
                TrialLength(indTrial) = size(tmpdat.trial{indTrial},2);
            end
            [val, idx] = min(TrialLength);
            for indTrial = 1:64
                tmpdat.trial{indTrial} = tmpdat.trial{indTrial}(:,1:val);
                tmpdat.time{indTrial} = tmpdat.time{idx};
            end
            
            %%  get artifact contaminated epochs & exclude epochs
            % includes: - THG_MWB_channel_x_epoch_artifacts_20140311
            %           - THG_FASTER_2_epoch_artifacts_20140302
            % recursive epoch exclusion!

            [tmpdat index] = THG_automatic_artifact_correction_trials_20170922(tmpdat);

            % write log
            fprintf(fid,'(2) automatic recursive bad epoch detection:\n');
            fprintf(fid,['MWB & FASTER: ' num2str(n_trl-length(index)) ' bad epoch(s) detected\n\n']);

            %%  get channel x epoch artifacts

            % cfg
            cfg.criterion = 3;
            cfg.recursive = 'yes';

            [index3 parm3 zval3] = THG_FASTER_4_channel_x_epoch_artifacts_20140302(cfg,tmpdat);

            % write log
            fprintf(fid,'(3) automatic single epoch/channel detection:\n');
            fprintf(fid,['FASTER:       ' num2str(sum(sum(index3))) ' channel(s) x trial(s) detected\n\n']);

            % clear cfg
            clear cfg

            %%  collect and save detected artifacts & artifact correction infos

            % include ArtDect.parameters

            % bad channels
            ArtDect.channels = badchan;

            % bad trials
            tmp  = zeros(n_trl,1); tmp(index,1) = 1;
            badtrl = find(tmp==0);
            ArtDect.trials  = badtrl; 
            clear tmp

            % bad single epoch(s)/channel(s) - after exclusion of bad epochs
            ArtDect.channels_x_trials = index3;

            % overview
            ind = [1:n_trl];
            ind(badtrl) = [];
            tmp = ones(length(tmpdat.label),n_trl);
            tmp(:,ind) = index3;
            tmp(badchan,:) = 1;
            ArtDect.channels_x_trials_all = tmp;
            clear tmp

            % save version
            ArtDect.version = 'JQK 20180123';

            % add to config
            config.ArtDect = ArtDect;

            % save config
            save([pn.History, IDs{id}, '_r',num2str(iRun), '_', condEEG, '_config'],'config')
            
            %%  finalize log

            % log
            fprintf(fid,'Artifact detection completed.\n');
            fprintf(fid,['Information saved to: ' IDs{id} '_config.mat\n\n']);
            fclose(fid);
        end % run
    catch ME
        warning('Error occured. Please check.');
        rethrow(ME)
        fprintf('\n ID not availble! Skip! \n')
        ID_unavailable{id,1} = (IDs{id});
    end
    
%end; clear id

end