createBecomeFeedback.m

%----------------------------
% SETUP
%----------------------------

clear
close all

subName = 'FOK0217'; % change subject id here
userName = 'dorothee_poehlchen'; % change your name here

gitdir = fullfile('C:\Users\',userName,'Documents\GitHub\becomeFeedback');
basedir = 'O:\Psychophys\Dreem';
diarydir = fullfile(basedir, 'Actigraphy\Raw\Sleep Diaries');
actidir = fullfile(basedir, 'Actigraphy\Raw\Clean Acti Data'); 
ecgdir = fullfile(basedir, 'Actigraphy\Raw\ECG_RR');
dreemdir = fullfile(basedir,'data\BeCOME' );
outdir = fullfile(basedir,'data\BeCOME_feedback' );
fundir = fullfile(gitdir, 'functions');
libsdir = fullfile(gitdir, 'libs');

addpath(genpath(fundir));
addpath(genpath(libsdir));


%----------------------------
% SETUP
%----------------------------

timeStep = minutes(10); % downsample data from 30s to 10m timesteps
missingDataThreshold = 6; % missing value if 6 timeSteps at least are 0
timeCenteredMean = hours(24); % moving mean of 24 hours
sleepBoutThreshold = 3; % equals to 30 min
percTreshold = 15; % everyoriginal datapoint < 15% of moving mean = sleep
sleepGapLength = 3; % correlation gap (finds correlation peak)
centeredBoutMean = hours(4); % last step from correl data to only 1 onset and offset per night --> 4 hour moving mean
meanTreshold = 0.4; % for the moving mean on the binary sleep bouts to smooth them
color.sleepSmoothed = [240/255,128/255,128/255]; %salmon color = night sleep episodes
color.acti = [112/255,128/255,144/255]; % gray = actigraphy raw data
color.sleepCorr = [255/255,215/255,0/255]; % gold = sleep determined by correlation filter --> showing sleep fragmentation
color.ecg = [1/255,0/255,1/255]; %sea green = ecg bpm data

HRVparams       = InitializeHRVparams('ActigraphyECG'); % HRV paraeters for calculation %%%
HRVparams.Fs                = 500;  % sampling frequency
HRVparams.windowlength      = 300;  % Default: 300, seconds
HRVparams.increment         = 60;   % 60 second increments
HRVparams.freq.method = 'fft';      % Default: 'lomb'

%----------------------------
% Readout actigraphy and ecg
%----------------------------

[diarySleepTable, acti, ecgData] = loadSubjectData(diarydir, actidir, ecgdir, subName);

if (isempty(ecgData.rr)) && (~isempty(ecgData.rawData))
    ecgData = convertToRR (ecgData, HRVparams, subName,ecgdir);     % Convert ECG waveform in rr intervals (if its a new data set)
    HRVMetrics = calcHRVvariables (ecgData.rr,ecgData.t,HRVparams,subName,ecgData.hdr,timeStep);
elseif (~isempty(ecgData.rr))
    HRVMetrics = calcHRVvariables (ecgData.rr,ecgData.t,HRVparams,subName,ecgData.hdr,timeStep);
else
    HRVMetrics = [];    
end


%----------------------------
% Calculate sleep bouts from actigraphy 
%----------------------------

calcSleepFromActi 


%----------------------------
% Plot actigraphy and ecg figures 
%----------------------------

[figures, ecgFig, sleepECGAll] = ReportFigures(sleepECG,cleanedActi,HRVMetrics);
doublePlot = doubleAreaLinePlot(sleepECGAll);



%----------------------------
% Get dreem data
%----------------------------

[dreemHypno, dreemReport] = loadSubjectDataDreemSD(dreemdir, subName); % if there is no dreem data COMMENT THIS LINE OUT!
[allinonePhysSleep] = getPhysiologyDataDreem (dreemReport);
nightData = synchronize (dreemHypno,allinonePhysSleep,'first','previous');
figuresNight = dreemNightFigures(nightData);




%----------------------------
% Create the final report 
%----------------------------
createBecomeReport


%----------------------------
% Save report and data
%----------------------------
mkdir(fullfile(outdir,subName))
save(fullfile(outdir,subName,[subName,'rpt']),'rpt')