PhysioNet Cardiovascular Signal Toolbox 1.0.0

%	OVERVIEW:
%       This is demo for PhysioNet Cardiovascular Signal Toolbox 
%       using RR intervals with annotations. 
%       Provided data are a subset from the MIT Physionet 
%       NSR dataset, which contains long-term ECG recordings of subjects 
%       in normal sinus rhythm.
%       It shows how to automaticly import multiple files from a folder, 
%       perfrom the HRV analysis on each of them and then store the results 
%       in .csv format.  
%       It uses the default parameters in the configuration file using 
%       'demo_NSR' option : InitializeHRVparams('demo_NSR').
%
%   OUTPUT:
%       HRV Metrics exported to .cvs files
%
%   DEPENDENCIES & LIBRARIES:
%       https://github.com/cliffordlab/PhysioNet-Cardiovascular-Signal-Toolbox
%   REFERENCE: 
%       Vest et al. "An Open Source Benchmarked HRV Toolbox for Cardiovascular 
%       Waveform and Interval Analysis" Physiological Measurement (In Press), 2018. 
%	REPO:       
%       https://github.com/cliffordlab/PhysioNet-Cardiovascular-Signal-Toolbox
%   ORIGINAL SOURCE AND AUTHORS:     
%       Giulia Da Poian   
%	COPYRIGHT (C) 2018 
%   LICENSE:    
%       This software is offered freely and without warranty under 
%       the GNU (v3 or later) public license. See license file for
%       more information
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

clear; clc; close all;

% Remove old files generated by this demo
OldFolder = [pwd,filesep, 'OutputData', filesep, 'ResultsNSR'];
if exist(OldFolder, 'dir')
    rmdir(OldFolder, 's');
    fprintf('Old Demo Folder deleted \n \n');
end


% Initialize settings for demo
HRVparams = InitializeHRVparams('demo_NSR');  
HRVparams.MSE.on = 0; % No MSE analysis for this demo
HRVparams.DFA.on = 0; % No DFA analysis for this demo
HRVparams.HRT.on = 0; % No HRT analysis for this demo
HRVparams.output.separate = 0;   % For this demo write all the results in one file 


% Check for a list of files to be analyzed in current directory in .dat format
[subjectIDs,filesTBA] = GenerateListOfFilesTBA(HRVparams.ext, HRVparams.readdata,[]);

% Prepare for parallel loop by eliminating variables
clear nummatchingfiles x i filename flag match
numsub = length(subjectIDs);
notAnalyzed = 0;

% NOTE: This loop can be run in parallel by changing the loop to a parfor
% loop.
for i_patient = 1:numsub   
    
    thisPatient = strcat(HRVparams.readdata, filesep, subjectIDs(i_patient));
    try
        
        % 1. Import Patient Data
        RRwindowStartIndices = [];
        tNN = [];
        NN = [];
        [samples,annotations] = read_ann(thisPatient{1},HRVparams.ext);
        rr = diff(samples)./HRVparams.Fs; 
        t = cumsum(rr);
        
        % Demo keeps only the first 2h 
        
        rr = rr(t<60*60*2);
        t = t(t<60*60*2);
               
        % 2. Perform HRV analysis on the RR intervals
        [results, resFilenameHRV] = Main_HRV_Analysis(rr,t,'RRIntervals',HRVparams,subjectIDs(i_patient),annotations);
        currentFile = [HRVparams.writedata filesep resFilenameHRV.HRV '.csv'];

        fprintf('\n');
    catch
       
        results = NaN;
        col_titles = {'NaN'};
        currentFile = '';
        notAnalyzed = 1;
        fprintf('Error on subject %s \n', char(subjectIDs(i_patient)));    

    end
    
end


% 3. Compare generated output file with the reference one

referenceFile = ['ReferenceOutput' filesep 'NSR_HRV_allwindows_allpatients.csv'];
testHRV = CompareOutput(currentFile,referenceFile);

if testHRV
    fprintf('\n ** DemoAnnotatedData: TEST SUCCEEDED ** \n ')
elseif notAnalyzed == 0
    fprintf('\n ** DemoAnnotatedData: TEST FAILED ** \n')
    fprintf('Error: generated output does not match reference \n')
elseif notAnalyzed == 1
    fprintf('\n** DemoAnnotatedData: TEST FAILED ** \n')
    fprintf('Error: analysis not performed \n');    
end