export_hypnogram_backup.m

function export_hypnogram(cfg)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% function export_hypnogram(cfg)
%
% Searches through patient directly, finds hypnogram files, finds those
% NeuraLynx directories that overlap with hypnogram files, aligns MicroMed
% with NeuraLynx data, and writes new Events.mrk files for Muse in all
% NeuraLynx directories that contain hypnogram data.
%
% Necessary fields:
%
% cfg.patientdir            = [path to patient data, one above /eeg and /eegmicromed]
% cfg.hyp.micromedchannel   = [micromed channel to use for alignment]
% cfg.imagesavedir          = [path to directory in which to save plots]
% cfg.prefix                = [string to prefix output figure, e.g. patient ID]
% cfg.hyp.backupdir         = [directory to backup Muse marker files]
%
% Example:
%
% cfg                       = [];
% cfg.patientdir            = '/network/lustre/iss01/epimicro/patients/raw/pat_02711_1193';
% cfg.hyp.micromedchannel   = 'F3p6';
% cfg.imagesavedir          = '/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/images/hspike';
% cfg.prefix                = 'P1-';
% cfg.hyp.backupdir         = '/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/markerbackup';
% export_hypnogram(cfg);
%
% Note:
% Names of markers that contain a space (' ') or minus ('-') will be
% replaced by an underscore ('_').
%
% Dependencies: writeMuseMarkers.m, dir2.m, recent FieldTrip version
%
% (c) Stephen Whitmarsh (stephen.whitmarsh@gmail.com)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

feature('DefaultCharacterSet', 'UTF8') %# for all Character support, or 'CP1252'

% list of all hypnogram files in MicroMed directory
micromed_hypnfilelist                   = dir2(fullfile(cfg.patientdir,'eegmicromed','*.hypn'));

% get some info about the 'real' time of recording the MicroMed data
for ifile = 1 : size(micromed_hypnfilelist,1)
    
    [~,name,~]                              = fileparts(micromed_hypnfilelist(ifile).name);
    fname                                   = fullfile(cfg.patientdir,'eegmicromed',[name,'.bni']);
    hdrMM                                   = ft_read_header(fullfile(cfg.patientdir,'eegmicromed',[name,'.TRC']));
    
    opts                                    = detectImportOptions(fname,'FileType','text','Delimiter','=');
    opts.VariableNames                      = {'key','value'};
    opts.Delimiter                          = {'='};
    opts.VariableTypes                      = {'char','char'};
    T2                                      = readtable(fname,opts);
    micromed_date{ifile}                    = datetime(cell2mat(T2.value(find(strcmp(T2.key,'Date')))),'Format','MM/dd/yyyy');
    micromed_time{ifile}                    = datetime(cell2mat(T2.value(find(strcmp(T2.key,'Time')))),'Format','HH/mm/ss');
    micromed_starttime{ifile}               = datetime([cell2mat(T2.value(find(strcmp(T2.key,'Date')))), cell2mat(T2.value(find(strcmp(T2.key,'Time'))))],'Format','MM/dd/yyyyHH:mm:ss');
    micromed_starttime{ifile}               = datetime(micromed_starttime{ifile},'Format','yyy/MM/dd HH:mm:ss');
    micromed_endtime{ifile}                 = micromed_starttime{ifile} + seconds(hdrMM.nSamples / hdrMM.Fs);
end

% overview and timing of neuralynx data
neuralynx_dirlist = dir2(fullfile(cfg.patientdir,'eeg'));
neuralynx_dirlist = neuralynx_dirlist([neuralynx_dirlist.isdir]);

% add "real time" of computer clock to neuralynx file time
for idir = 1 : size(neuralynx_dirlist,1)
    neuralynx_datafiles{idir}   = dir2(fullfile(neuralynx_dirlist(idir).folder,neuralynx_dirlist(idir).name,'*m*.ncs'));
    neuralynx_txtfiles{idir}    = dir2(fullfile(neuralynx_dirlist(idir).folder,neuralynx_dirlist(idir).name,'*.txt'));
    neuralynx_hdr{idir}         = ft_read_header(fullfile(neuralynx_dirlist(idir).folder,neuralynx_dirlist(idir).name,neuralynx_datafiles{idir}(1).name)); % read header from first ncs file
    
    f = fopen(fullfile(neuralynx_txtfiles{idir}(1).folder,neuralynx_txtfiles{idir}(1).name));
    clear timestring
    while 1
        tline = fgetl(f);
        if ~ischar(tline), break, end
        searchstring = '## Time Opened (m/d/y)';
        try
            if strcmp(tline(1:length(searchstring)),searchstring)
                neuralynx_timestring = tline;
                disp('Great, found timestamp in header file');
                break
            end
        catch
            disp('Warning: something weird happened reading the txt time');
        end
    end
    fclose(f);
    
    neuralynx_timestring         = strsplit(neuralynx_timestring);
    neuralynx_headerdate{idir}   = [cell2mat(neuralynx_timestring(5)) ' ' cell2mat(neuralynx_timestring(7))];
    neuralynx_starttime{idir}    = datetime(neuralynx_headerdate{idir},'Format','MM/dd/yy HH:mm:ss.SSS');
    neuralynx_endtime{idir}      = neuralynx_starttime{idir} + seconds(neuralynx_hdr{idir}.nSamples /neuralynx_hdr{idir}.Fs);
end

% find overlap between micromed and neuralynx files
for iMicroMed = 1 : size(micromed_hypnfilelist,1)
    hasoverlap{iMicroMed} = [];
    
    % Search all neuralynx files
    for iNeuraLynx = 1 : size(neuralynx_datafiles,2)
        % look for any marker in the MicroMed marker file that corresponds
        % with the approximate time recorded in the NeuraLynx datafile
        try
            if isbetween(micromed_starttime{iMicroMed},neuralynx_starttime{iNeuraLynx},neuralynx_endtime{iNeuraLynx}) || isbetween(micromed_endtime{iMicroMed},neuralynx_starttime{iNeuraLynx},neuralynx_endtime{iNeuraLynx})
                hasoverlap{iMicroMed} = [hasoverlap{iMicroMed}, iNeuraLynx];
            end
        catch
        end
    end
    
    % check if there is a neuralynx file for every hypnogram file
    if isempty(hasoverlap{iMicroMed})
        fprintf('OOPS! Could not find Neuralynx file that overlaps with %s',micromed_hypnfilelist(iMicroMed).name);
    end
end

% loop over all micromed files
for iMicroMed = 1 : size(micromed_hypnfilelist,1)
    
    [~,name,~]      = fileparts(micromed_hypnfilelist(iMicroMed).name);
    cfgtemp         = [];
    cfgtemp.dataset = fullfile(micromed_hypnfilelist(iMicroMed).folder,[name,'.TRC']);
    cfgtemp.channel = cfg.hyp.micromedchannel;
    dat_MM          = ft_preprocessing(cfgtemp);
    
    dat_NL_concat   = [];
    MM_title        = [cfgtemp.dataset, ': ', cfgtemp.channel];
    NL_title        = [];
    
    % loop over (multiple) overlapping neuralynx files
    for idir = [hasoverlap{iMicroMed}]
        
        % figure out the same channel name for neuralynx
        channelnr = 0;
        l = dir2(fullfile(neuralynx_datafiles{idir}(iMicroMed).folder,'*.ncs'));
        
        for i = 1 : size(l,1)
            if findstr(l(i).name,['_',dat_MM.label{1}(1:end-1), '_', dat_MM.label{1}(end)])
                channelnr = i;
                fprintf('Found match: %s : %s\n',l(i).name,['_',dat_MM.label{1}(1:end-1), '_', dat_MM.label{1}(end)]);
            end
        end
        if channelnr == 0
            fprintf('Could not find similar channel\n');
        end
        
        cfgtemp             = [];
        cfgtemp.dataset     = fullfile(neuralynx_datafiles{idir}(1).folder,l(channelnr).name);
        cfgtemp.channel     = 'all';
        dat_NL              = ft_preprocessing(cfgtemp);
        if ~isempty(NL_title)
            NL_title = [NL_title, '\n'];
        end
        NL_title            = [NL_title, cfgtemp.dataset];
        
        % resample neuralynx to same samplerate of micromed data
        cfgtemp             = [];
        cfgtemp.resamplefs  = hdrMM.Fs;
        dat_NL              = ft_resampledata(cfgtemp,dat_NL);
        dat_NL_concat       = [dat_NL_concat dat_NL.trial{1}];
    end
    
    % neuralynx data is inverted from micromed
    dat_NL_concat = -dat_NL_concat;
    D = finddelay(dat_MM.trial{1},dat_NL_concat);
    
    X1 = 1:size(dat_MM.trial{1},2);
    X2 = (1:size(dat_NL_concat,2)) - D;
    
    fig = figure;
    fig.Renderer = 'Painters';
    ax1 = subplot(2,1,1);
    plot(X1,dat_MM.trial{1});
    title(MM_title,'Interpreter','none');
    ax = gca;
    ax.FontSize = 8;
    axis tight
    
    ax2 = subplot(2,1,2);
    plot(X2,dat_NL_concat);
    title(sprintf(NL_title),'Interpreter','none');
    ax = gca;
    ax.FontSize = 8;
    axis tight
    
    linkaxes([ax1,ax2]);
    set(fig,'PaperOrientation','landscape');
    set(fig,'PaperUnits','normalized');
    set(fig,'PaperPosition', [0 0 1 1]);
    
    [~,name,~] = fileparts(micromed_hypnfilelist(iMicroMed).name);
    print(fig, '-dpdf', fullfile(cfg.hyp.imagesavedir,[cfg.prefix,'alignment_',name,'.pdf']));
    print(fig, '-dpng', fullfile(cfg.hyp.imagesavedir,[cfg.prefix,'alignment_',name,'.png']),'-r600');
    close all
    
    % read hypnogram, remove sample
    hyp = readtable(fullfile(micromed_hypnfilelist(iMicroMed).folder,micromed_hypnfilelist(iMicroMed).name),'FileType','text');
    
    % apply synchronization
    hyp.startSec    = round(hyp.startSec + (D / hdrMM.Fs),4);
    hyp.endSec      = round(hyp.endSec   + (D / hdrMM.Fs),4);
    
    % take the Neurlynx data headerinfo from the first file to know how many samples the file is
    filelength = 0;
    for idir = [hasoverlap{iMicroMed}]
        flist = dir2(fullfile(neuralynx_dirlist(idir).folder,neuralynx_dirlist(idir).name,'*.ncs'));
        datafile = fullfile(flist(1).folder,flist(1).name);
        hdr = ft_read_header(datafile);
        filelength = [filelength, hdr.nSamples / hdr.Fs];
    end
    
    % figure out which hypnogram markers belong to which Neuralynx file
    filelengthc = cumsum(filelength);
    hyp.startfilenr = zeros(height(hyp),1);
    hyp.endfilenr = zeros(height(hyp),1);
    for i = 1 : size(filelength,2)
        hyp.startfilenr(hyp.startSec >= filelengthc(i)) = hyp.startfilenr(hyp.startSec >= filelengthc(i)) + 1;
        hyp.endfilenr(hyp.endSec >= filelengthc(i)) = hyp.endfilenr(hyp.endSec >= filelengthc(i)) + 1;
    end
    
    % split those hypnogram markers span over multiple files
    if any(hyp.startfilenr ~= hyp.endfilenr)
        for imarker = find(hyp.startfilenr ~= hyp.endfilenr)
            hyp(end+1,:) = hyp(imarker,:);
            hyp.startSec(end) = filelengthc(hyp.endfilenr(imarker));
            hyp.startfilenr(end) = hyp.endfilenr(end);
            hyp.endSec(imarker) = filelengthc(hyp.endfilenr(imarker));
            hyp.endfilenr(imarker) = hyp.startfilenr(imarker);
        end
    end
    
    % adjust timing of those hypnogram periods falling in multiple files
    for i = 1 : height(hyp)
        hyp.startSec(i) = hyp.startSec(i) - filelengthc(hyp.startfilenr(i));
        hyp.endSec(i)   = hyp.endSec(i) - filelengthc(hyp.startfilenr(i));
    end
    
    % add to Muse events file
    hypi = 1;
    for idir = [hasoverlap{iMicroMed}]
        
        % first read Muse events file
        name_mrk = fullfile(neuralynx_dirlist(idir).folder,neuralynx_dirlist(idir).name,'Events.mrk');
        
        if ~exist(name_mrk)
            error('%s not found!', name_mrk);
        end
        f = fopen(name_mrk, 'rt');
        markfile = {};
        while true
            l = fgetl(f);
            if ~ischar(l)
                break
            end
            markfile{end + 1} = l;
        end
        fclose(f);
        
        if isempty(markfile)
            error('\n\n %s is empty!!! \n\n',name_mrk);
        end
        nmarkers        = str2num(markfile{strmatch('NUMBER OF MARKERS:',       markfile, 'exact') + 1});
        classgroupid    = markfile(strmatch('CLASSGROUPID:',                    markfile, 'exact') + 1);
        name            = markfile(strmatch('NAME:',                            markfile, 'exact') + 1);
        comment         = markfile(strmatch('COMMENT:',                         markfile, 'exact') + 1);
        color           = markfile(strmatch('COLOR:',                           markfile, 'exact') + 1);
        editable        = markfile(strmatch('EDITABLE:',                        markfile, 'exact') + 1);
        classid         = markfile(strmatch('CLASSID:',                         markfile, 'exact') + 1);
        nrEvents        = str2num(char(markfile(strmatch('NUMBER OF SAMPLES:',  markfile, 'exact') + 1)));
        
        % Get the events, time is in seconds from onset of file
        clear marks
        j = strmatch('LIST OF SAMPLES:', markfile, 'exact') + 2;
        for imarker = 1 : nmarkers
            marks{imarker} = str2num(char(markfile(j(imarker):j(imarker) + nrEvents(imarker) - 1)));
            
            % Convert from index origin 0 to 1
            if nrEvents(imarker) ~= 0
                marks{imarker}(:, 1) = marks{imarker}(:, 1) + 1;
            end
        end
        
        % put data back into structure to write later
        clear MuseStruct
        for imarker = 1 : nmarkers
            name{imarker} = strrep(name{imarker},'-','_'); % cant make fieldnames with minusses
            MuseStruct.markers.(name{imarker}).comment        = comment{imarker};
            MuseStruct.markers.(name{imarker}).color          = color{imarker};
            MuseStruct.markers.(name{imarker}).editable       = editable{imarker};
            MuseStruct.markers.(name{imarker}).classid        = classid{imarker};
            MuseStruct.markers.(name{imarker}).classgroupid   = classgroupid{imarker};
            for ievent = 1 : nrEvents(imarker)
                MuseStruct.markers.(name{imarker}).trialnum(ievent) = marks{imarker}(ievent,1);
                MuseStruct.markers.(name{imarker}).synctime(ievent) = marks{imarker}(ievent,2);
            end
        end
        
        clear markers
        
        % select those hypnogram markers that belong the the current Muse (neuralynx) marker file
        hyp_file = hyp(hyp.startfilenr == hypi,:);
        
        for label = unique(hyp_file.stage)'
            
            if strcmp(label,'BEGIN')
                
                MuseStruct.markers.StartHypnogram.synctime       = hyp_file.startSec(strcmp(hyp_file.stage, label));     % replace space with underscore
                MuseStruct.markers.StartHypnogram.trialnum       = 0;  
                MuseStruct.markers.StartHypnogram.classgroupid   = '+3';
                MuseStruct.markers.StartHypnogram.comment        = 'Exported from hypnogram';
                MuseStruct.markers.StartHypnogram.editable       = 'Yes';
                MuseStruct.markers.StartHypnogram.classid        = '+666'; % will be replaced by writeMuseMarkers.m
                MuseStruct.markers.StartHypnogram.color          = 'black';
            end
            
            if strcmp(label,'END')
                
                MuseStruct.markers.EndHypnogram.synctime        = hyp_file.startSec(strcmp(hyp_file.stage, label));     % replace space with underscore
                MuseStruct.markers.EndHypnogram.trialnum        = 0;  
                MuseStruct.markers.EndHypnogram.classgroupid    = '+3';
                MuseStruct.markers.EndHypnogram.comment         = 'Exported from hypnogram';
                MuseStruct.markers.EndHypnogram.editable        = 'Yes';
                MuseStruct.markers.EndHypnogram.classid         = '+666'; % will be replaced by writeMuseMarkers.m
                MuseStruct.markers.EndHypnogram.color           = 'black';
            end
            
            % for those markers that have a duration
            if hyp_file.startSec(strcmp(hyp_file.stage, label)) ~= hyp_file.endSec(strcmp(hyp_file.stage, label))
                
                MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).synctime       = hyp_file.startSec(strcmp(hyp_file.stage, label));     % replace space with underscore
                MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).trialnum       = zeros(size(MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).synctime));  % replace space with underscore
                MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).classgroupid   = '+3';
                MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).comment        = 'Exported from hypnogram';
                MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).editable       = 'Yes';
                MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).classid        = '+666'; % will be replaced by writeMuseMarkers.m
                
                switch label{1}
                    case 'AWAKE'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).color = 'cyan';
                    case 'PHASE 1'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).color = 'green';
                    case 'PHASE 2'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).color = 'blue';
                    case 'PHASE 3'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).color = 'red';
                    case 'PHASE 4'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).color = 'purple';
                    otherwise
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__START__']).color = 'black';
                end
                
                MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).synctime     = hyp_file.endSec(strcmp(hyp_file.stage, label));     % replace space with underscore
                MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).trialnum     = zeros(size(MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).synctime));  % replace space with underscore
                MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).classgroupid = '+3';
                MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).comment      = 'Exported from hypnogram';
                MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).editable     = 'Yes';
                MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).classid      = '+666'; % will be replaced by writeMuseMarkers.m
                
                switch label{1}
                    case 'AWAKE'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).color = 'yellow';
                    case 'PHASE 1'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).color = 'green';
                    case 'PHASE 2'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).color = 'blue';
                    case 'PHASE 3'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).color = 'red';
                    case 'PHASE 4'
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).color = 'purple';
                    otherwise
                        MuseStruct.markers.([strrep(label{1},' ','_'), '__END__']).color = 'black';
                end
                
%             else
%                 MuseStruct.markers.(strrep(label{1},' ','_')).synctime      = hyp_file.endSec(strcmp(hyp_file.stage, label));  % replace space with underscore
%                 MuseStruct.markers.(strrep(label{1},' ','_')).trialnum      = zeros(size(MuseStruct.markers.(strrep(label{1},' ','_')).synctime));  % replace space with underscore
%                 MuseStruct.markers.(strrep(label{1},' ','_')).classgroupid  = '+3';
%                 MuseStruct.markers.(strrep(label{1},' ','_')).comment       = 'Exported from hypnogram';
%                 MuseStruct.markers.(strrep(label{1},' ','_')).editable      = 'Yes';
%                 MuseStruct.markers.(strrep(label{1},' ','_')).classid       = '+666'; % will be replaced by writeMuseMarkers.m
%                 switch label{1}
%                     case 'AWAKE'
%                         MuseStruct.markers.(strrep(label{1},' ','_')).color = 'yellow';
%                     case 'PHASE 1'
%                         MuseStruct.markers.(strrep(label{1},' ','_')).color = 'green';
%                     case 'PHASE 2'
%                         MuseStruct.markers.(strrep(label{1},' ','_')).color = 'blue';
%                     case 'PHASE 3'
%                         MuseStruct.markers.(strrep(label{1},' ','_')).color = 'red';
%                     case 'PHASE 4'
%                         MuseStruct.markers.(strrep(label{1},' ','_')).color = 'purple';
%                     otherwise
%                         MuseStruct.markers.(strrep(label{1},' ','_')).color = 'black';
%                 end
            end
        end
        
        % backup markerfile
        if ~exist(cfg.hyp.backupdir,'DIR')
            error('Backup directory does not exist');
        end
        if ~exist(fullfile(cfg.hyp.backupdir,neuralynx_dirlist(idir).name),'DIR')
            fprintf('Creating directory: %s\n',fullfile(cfg.hyp.backupdir,neuralynx_dirlist(idir).name));
            eval(sprintf('!mkdir %s',fullfile(cfg.hyp.backupdir,neuralynx_dirlist(idir).name)));
        end
        fname_backup = sprintf('Events_%s.mrk', datestr(now, 'mm-dd-yyyy_HH-MM-SS'));
        eval(sprintf('!cp %s %s',name_mrk,fullfile(cfg.hyp.backupdir,neuralynx_dirlist(idir).name,fname_backup)));
        fprintf('Succesfully backed up markerfile to %s',fullfile(cfg.hyp.backupdir,neuralynx_dirlist(idir).name,fname_backup));
        
        % write new event structure
%         fname_out = fullfile(neuralynx_dirlist(idir).folder,neuralynx_dirlist(idir).name,'Events.mrk');
        fname_out = fullfile(cfg.hyp.markerdir,neuralynx_dirlist(idir).name,'Events.mrk');
        
        writeMuseMarkers(MuseStruct, fname_out);
        hypi = hypi + 1;
    end
    
end % micromed files