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InitializeHRVparams.m
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InitializeHRVparams.m
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function HRVparams = InitializeHRVparams(project_name)
%
% settings = InitializeHRVparams('project_name')
%
% OVERVIEW:
% This file stores settings and should be configured before
% each use of the PhysioNet Cardiovascular Signal Toolbox:
% 1. Project Specific Input/Output Data type and Folders
% 2. How much does the user trust the data
% 3. Global Settings (Window Size) for signal segmentation
% 4. Quality Threshold Settings
% 5. Debug Settings
% 6. SQI Settings
% 7. Preprocess Settings
% 8. AF Detection Settings
% 9. Time Domain Analysis Settings
% 10. Frequency Domain Analysis Settings
% 11. SDANN and SDNNI Analysis Settings
% 12. PRSA Analysis Settings
% 13. Peak Detection Settings
% 14. Entropy and Multiscale Entropy - MSE - Settings
% 15. Detrended Fluctuation Analysis - DFA - Settings
% 16. Poincar� plot - Settings
% 17. Heart Rate Turbulence (HRT) - Settings
% 18. Output Settings
% 19. Time of Process and Filename to Save Data
%
% INPUT:
% project_name = a string with the name of the project - this
% will determine the naming convention of file folders
%
% OUTPUT:
% HRVparams - struct of various settings for the hrv_toolbox analysis
%
% DEPENDENCIES & LIBRARIES:
% PhysioNet Cardiovascular Signal Toolbox
% 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:
% Adriana N. Vest
% Giulia Da Poian
% Dependent scripts written by various authors
% (see functions for details)
% 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
%%
if isempty(project_name)
project_name = 'none';
end
% Set up input options for a specific project
switch project_name
% Define new project name and parameters
case 'MyProjectName' % Update with your project name
HRVparams.Fs = NaN; % Spacify sampling frequency
HRVparams.readdata = ''; % (Optional) Specify name for data input folder
HRVparams.writedata = ''; % (Optional) Specify name for data output folder
HRVparams.datatype = ''; % (Optional) Spacify Data type of input
HRVparams.ext = ''; % (Optional) Spacify file extension of input (e.g., 'mat','qrs')
% Existing demo projects
case 'MVanalysis' % Morphological variability analysis ECG
HRVparams.Fs = 1000;
HRVparams.readdata = '';
HRVparams.writedata = '';
HRVparams.datatype = '';
HRVparams.ext = '';
case 'demo_NSR' % Parameters for demo using MIT nsr data
HRVparams.readdata = strcat('TestData', filesep, 'Physionet_nsr2db');
HRVparams.writedata = strcat('OutputData', filesep, 'ResultsNSR');
HRVparams.ext = 'ecg';
HRVparams.Fs = 125;
case 'demo_RRgen'
HRVparams.writedata = strcat('OutputData', filesep, 'ResultsRRgen');
HRVparams.Fs = 125;
HRVparams.demo.length = 5*60*60; % Length of demo RR intervals in seconds
HRVparams.demo.pe = 0.0003; % Probability of ectopy ~ 1 per hr
HRVparams.demo.pn = 0.0048; % Probability of noise ~ 16 per hr
HRVparams.demo.seed = 1; % Seed for RRGEN
case 'demoICU' % Parameters for ICU demo
HRVparams.readdata = strcat('TestData');
HRVparams.writedata = strcat('OutputData', filesep, 'ResultsICU');
HRVparams.ext = 'mat';
HRVparams.Fs = 128;
case 'demoAF' % Parameters for AF demo
HRVparams.readdata = strcat('TestData');
HRVparams.writedata = strcat('OutputData', filesep, 'ResultsAFData');
HRVparams.ext = 'mat';
HRVparams.Fs = 128;
case 'demoHRT' % Parameters for HRT demo
HRVparams.readdata = strcat('TestData', filesep, 'Physionet_nsr2db');
HRVparams.writedata = strcat('OutputData', filesep, 'ResultsHRT');
HRVparams.Fs = 128;
case 'demoPVC' % Parameters for PVC demo
HRVparams.readdata = strcat('TestData', filesep, 'mitdb-Arrhythmia');
HRVparams.writedata = strcat('OutputData', filesep, 'ResultsPVC');
HRVparams.Fs = 360;
otherwise % Default
HRVparams.Fs = NaN; % Spacify sampling frequency
HRVparams.writedata = 'HRV_Output'; % (Optional) Specify name for data output folder
end
if isempty(HRVparams.writedata)
% Default data OUTPUT folder name based on project name
HRVparams.writedata = strcat(project_name,'_Results');
fprintf('New OUTPUT folder: "%s"\n', HRVparams.writedata)
mkdir(HRVparams.writedata); % Create output folder and
elseif ~exist([pwd filesep HRVparams.writedata], 'dir')
fprintf('New OUTPUT folder: "%s"\n',HRVparams.writedata)
mkdir(HRVparams.writedata); % Create output folder and
end
addpath(genpath(HRVparams.writedata)); % Add folder to search path
%% 2. How much does the user trust the data:
% This setting determines how stringently filtered the data is prior to
% calculating HRV metrics. Raw ECG or Pulse data that has been labeled
% using a peak detector (like jqrs) would require the most stringent
% filtering, whereas RR interval data that has been reviewed by a human
% technician would require the least amount of filtering.
% - qrs detection no beats labeled - most stringent filters
% - automatic beat detection beat typed - moderately stringent filtered
% - hand corrected - least filtered, maybe no filter
% EXPLAIN THE THRESHOLDS BETTER
% ADD THIS TO A DEMO
HRVparams.data_confidence_level = 1;
% 1 - raw data with automatic beat detection
% 2 - raw data with automatic beat detection, but beat typed (ie N, SV,etc)
% 3 - technician reviewed data
% * ^^^^ NOT YET IN USE ^^^^ *
%% 3. Global Settings (Window Size)
HRVparams.windowlength = 300; % Default: 300, seconds
HRVparams.increment = 30; % Default: 30, seconds increment
HRVparams.numsegs = 5; % Default: 5, number of segments to collect with lowest HR
HRVparams.RejectionThreshold = .20; % Default: 0.2, amount (%) of data that can be rejected before a
% window is considered too low quality for analysis
HRVparams.MissingDataThreshold = .15; % Default: 0.15, maximum percentage of data allowable to be missing
% from a window .15 = 15%
%% 5. Debug Settings
HRVparams.rawsig = 0; % Load raw signal if it is available for debugging
HRVparams.debug = 0;
%% 6. SQI Analysis Settings
HRVparams.sqi.LowQualityThreshold = 0.9; % Default: 0.9, Threshold for which SQI represents good data
HRVparams.sqi.windowlength = 10; % Default: 10, seconds, length of the comparison window
HRVparams.sqi.increment = 1; % Default: 1, seconds
HRVparams.sqi.TimeThreshold = 0.1; % Default: 0.1, seconds
HRVparams.sqi.margin = 2; % Default: 2, seconds, Margin time not include in comparison
%% 7. Preprocess Settings
HRVparams.preprocess.figures = 0; % Figures on = 1, Figures off = 0
HRVparams.preprocess.gaplimit = 2; % Default: 2, seconds; maximum believable gap in rr intervals
HRVparams.preprocess.per_limit = 0.2; % Default: 0.2, Percent limit of change from one interval to the next
HRVparams.preprocess.forward_gap = 3; % Default: 3, Maximum tolerable gap at beginning of timeseries in seconds
HRVparams.preprocess.method_outliers = 'rem'; % Default: 'rem', Method of dealing with outliers
% 'cub' = replace outlier points with cubic spline method
% 'rem' = remove outlier points
% 'pchip' = replace with pchip method
HRVparams.preprocess.lowerphysiolim = 60/160; % Default: 60/160
HRVparams.preprocess.upperphysiolim = 60/30; % Default: 60/30
HRVparams.preprocess.method_unphysio = 'rem'; % Default: 'rem', Method of dealing with unphysiologically low beats
% 'cub' = replace outlier points with cubic spline method
% 'rem' = remove outlier points
% 'pchip' = replace with pchip method
% The following settings do not yet have any functional effect on
% the output of preprocess.m:
HRVparams.preprocess.threshold1 = 0.9 ; % Default: 0.9, Threshold for which SQI represents good data
HRVparams.preprocess.minlength = 30; % Default: 30, The minimum length of a good data segment in seconds
%% 8. AF Detection Settings and PVC detection
HRVparams.af.on = 1; % Default: 1, AF Detection On or Off
HRVparams.af.windowlength = 30; % Default: 30, Set to include ~30 beats in each window
HRVparams.af.increment = 30; % Default: 30, No overlap necessary in AF feat calc
HRVparams.PVC.qrsth = 0.1; % Default: 0.1, threshold for qrs detection
%% 9. Time Domain Analysis Settings
HRVparams.timedomain.on = 1; % Default: 1, Time Domain Analysis 1=On or 0=Off
HRVparams.timedomain.dataoutput = 0; % 1 = Print results to .txt file
% Anything else = utputs to return variables only
% returned variables
HRVparams.timedomain.alpha = 50 ; % Default: 50 ,In msec
HRVparams.timedomain.win_tol = .15; % Default: .15, Maximum percentage of data allowable
% to be missing from a window
%% 10. Frequency Domain Analysis Settings
HRVparams.freq.on = 1; % Default: 1, Frequency Domain Analysis 1=On or 0=Off
ULF = [0 .0033]; % Requires window > 300 s
VLF = [0.0033 .04]; % Requires at least 300 s window
LF = [.04 .15]; % Requires at least 25 s window
HF = [0.15 0.4]; % Requires at least 7 s window
HRVparams.freq.limits = [ULF; VLF; LF; HF];
HRVparams.freq.zero_mean = 1; % Default: 1, Option for subtracting the mean from the input data
HRVparams.freq.method = 'lomb'; % Default: 'lomb'
% Options: 'lomb', 'burg', 'fft', 'welch'
HRVparams.freq.plot_on = 0;
% The following settings are for debugging spectral analysis methods
HRVparams.freq.debug_sine = 0; % Default: 0, Adds sine wave to tachogram for debugging
HRVparams.freq.debug_freq = 0.15; % Default: 0.15
HRVparams.freq.debug_weight = .03; % Default: 0.03
% Lomb:
HRVparams.freq.normalize_lomb = 0; % Default: 0
% 1 = Normalizes Lomb Periodogram,
% 0 = Doesn't normalize
% Burg: (not recommended)
HRVparams.freq.burg_poles = 15; % Default: 15, Number of coefficients
% for spectral estimation using the Burg
% method (not recommended)
% The following settings are only used when the user specifies spectral
% estimation methods that use resampling : 'welch','fft', 'burg'
HRVparams.freq.resampling_freq = 7; % Default: 7, Hz
HRVparams.freq.resample_interp_method = 'cub'; % Default: 'cub'
% 'cub' = cublic spline method
% 'lin' = linear spline method
HRVparams.freq.resampled_burg_poles = 100; % Default: 100
%% 11. SDANN and SDNNI Analysis Settings
HRVparams.sd.on = 1; % Default: 1, SD analysis 1=On or 0=Off
HRVparams.sd.segmentlength = 300; % Default: 300, windows length in seconds
%% 12. PRSA Analysis Settings
HRVparams.prsa.on = 1; % Default: 1, PRSA Analysis 1=On or 0=Off
HRVparams.prsa.win_length = 30; % Default: 30, The length of the PRSA signal
% before and after the anchor points
% (the resulting PRSA has length 2*L)
HRVparams.prsa.thresh_per = 20; % Default: 20%, Percent difference that one beat can
% differ from the next in the prsa code
HRVparams.prsa.plot_results = 0; % Default: 0
HRVparams.prsa.scale = 2; % Default: 2, scale parameter for wavelet analysis (to compute AC and DC)
HRVparams.prsa.min_anch = 20; % Default: 20, minimum number of anchors point required to create the "average signal"
%% 13. Peak Detection Settings
% The following settings are for jqrs.m
HRVparams.PeakDetect.REF_PERIOD = 0.250; % Default: 0.25 (should be 0.15 for FECG), refractory period in sec between two R-peaks
HRVparams.PeakDetect.THRES = .6; % Default: 0.6, Energy threshold of the detector
HRVparams.PeakDetect.fid_vec = []; % Default: [], If some subsegments should not be used for finding the optimal
% threshold of the P&T then input the indices of the corresponding points here
HRVparams.PeakDetect.SIGN_FORCE = []; % Default: [], Force sign of peaks (positive value/negative value)
HRVparams.PeakDetect.debug = 0; % Default: 0
HRVparams.PeakDetect.ecgType = 'MECG'; % Default : MECG, options (adult MECG) or featl ECG (fECG)
HRVparams.PeakDetect.windows = 15; % Befautl: 15,(in seconds) size of the window onto which to perform QRS detection
%% 14. Entropy Settings
% Multiscale Entropy
HRVparams.MSE.on = 1; % Default: 1, MSE Analysis 1=On or 0=Off
HRVparams.MSE.windowlength = []; % Default: [], windows size in hours, default perform MSE on the entire signal
HRVparams.MSE.increment = []; % Default: [], window increment in hours
HRVparams.MSE.RadiusOfSimilarity = 0.15; % Default: 0.15, Radius of similarity (% of std)
HRVparams.MSE.patternLength = 2; % Default: 2, pattern length
HRVparams.MSE.maxCoarseGrainings = 20; % Default: 20, Maximum number of coarse-grainings
HRVparams.MSE.method = 'fir'; % Default 'fir', method use to generate the coarse-grain
% time series options 'fir', 'butter'
HRVparams.MSE.moment = 'mean'; % Default: 'mean', moment used to coarse-grain the time series
% options 'mean', 'variance'
HRVparams.MSE.constant_r = 1; % Default: 1, 1 use r as function of std of original time
% series, 0 compute r as function of std at each scale
% SampEn an ApEn
HRVparams.Entropy.on = 1; % Default: 1, MSE Analysis 1=On or 0=Off
HRVparams.Entropy.RadiusOfSimilarity = 0.15; % Default: 0.15, Radius of similarity (% of std)
HRVparams.Entropy.patternLength = 2; % Default: 2, pattern length
%% 15. DFA Settings
HRVparams.DFA.on = 1; % Default: 1, DFA Analysis 1=On or 0=Off
HRVparams.DFA.windowlength = []; % Default [], windows size in hours, default perform DFA on the entair signal
HRVparams.DFA.increment = []; % Default: [], window increment in hours
HRVparams.DFA.minBoxSize = 4 ; % Default: 4, Smallest box width
HRVparams.DFA.maxBoxSize = []; % Largest box width (default in DFA code: signal length/4)
HRVparams.DFA.midBoxSize = 16; % Medium time scale box width (default in DFA code: 16)
%% 16. Poincar� plot
HRVparams.poincare.on = 1; % Default: 1, Poincare Analysis 1=On or 0=Off
%% 17. Heart Rate Turbulence (HRT) - Settings
HRVparams.HRT.on = 1; % Default: 1, HRT Analysis 1=On or 0=Off
HRVparams.HRT.BeatsBefore = 2; % Default: 2, # of beats before PVC
HRVparams.HRT.BeatsAfter = 16; % Default: 16, # of beats after PVC and CP
HRVparams.HRT.GraphOn = 0; % Default: 0, do not plot
HRVparams.HRT.windowlength = 24; % Default 24h, windows size in hours
HRVparams.HRT.increment = 24; % Default 24h, sliding window increment in hours
HRVparams.HRT.filterMethod = 'mean5before'; % Default mean5before, HRT filtering option
%% 18. Output Settings
HRVparams.gen_figs = 0; % Generate figures
HRVparams.save_figs = 0; % Save generated figures
if HRVparams.save_figs == 1
HRVparams.gen_figs = 1;
end
% Format settings for HRV Outputs
HRVparams.output.format = 'csv'; % 'csv' - creates csv file for output
% 'mat' - creates .mat file for output
HRVparams.output.separate = 1; % Default : 1 = separate files for each subject
% 0 = all results in one file
HRVparams.output.num_win = []; % Specify number of lowest hr windows returned
% leave blank if all windows should be returned
% Format settings for annotations generated
HRVparams.output.ann_format = 'binary'; % 'binary' = binary annotation file generated
% 'csv' = ASCII CSV file generated
%% 19. Filename to Save Data
HRVparams.time = datestr(now, 'yyyymmdd'); % Setup time for filename of output
HRVparams.filename = [HRVparams.time '_' project_name];
%% Export Parameter as Latex Table
% Note that if you change the order of the parameters or add parameters
% this might not work
ExportHRVparams(HRVparams);
end