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function ppgOnsets = qppg(data,fs,from,to)
% This function is rewriten from wabp_pleth_new.c and wabp.c
% /* file wabp.c Wei Zong 23 October 1998
% Last revised: 9 April 2010 (by G. Moody)
% -----------------------------------------------------------------------------
% wabp: beat detector for arterial blood presure (ABP) signal
% Copyright (C) 1998-2010 Wei Zong
%
% This program is free software; you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free Software
% Foundation; either version 2 of the License, or (at your option) any later
% version.
%
% This program is distributed in the hope that it will be useful, but WITHOUT ANY
% WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
% PARTICULAR PURPOSE. See the GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License along with
% this program; if not, write to the Free Software Foundation, Inc., 59 Temple
% Place - Suite 330, Boston, MA 02111-1307, USA.
%
% You may contact the author by e-mail (wzong@mit.edu) or postal mail
% (MIT Room E25-505, Cambridge, MA 02139, USA). For updates to this software,
% please visit PhysioNet (http://www.physionet.org/).
% ------------------------------------------------------------------------------
%
% This program detects heart beats (pulse waveforms) in a continuous arterial
% blood pressure (ABP) signal. This version of wabp works best with ABP signals
% sampled at 125 Hz, but it can analyze ABPs sampled at any frequency
% using on-the-fly resampling provided by the WFDB library. 'wabp' has been
% optimized for adult human ABPs. For other ABPs, it may be necessary to
% experiment with the input sampling frequency and the time constants indicated
% below.
%
% `wabp' can process records containing any number of signals, but it uses only
% one signal for ABP pulse detection (by default, the lowest-numbered signal
% labelled `ABP', `ART', or `BP'; this can be changed using the `-s' option, see
% below).
%
% To compile this program under GNU/Linux, MacOS/X, MS-Windows, or Unix, use gcc:
% gcc -o wabp wabp.c -lwfdb
% You must have installed the WFDB library, available at
% http://www.physionet.org/physiotools/wfdb.shtml
% gcc is standard with GNU/Linux and is available for other platforms from:
% http://www.gnu.org/ (sources and Unix binaries)
% http://fink.sourceforge.net (Mac OS/X only)
% http://www.cygwin.com/ (MS-Windows only)
%
% For a usage summary, see the help text at the end of this file. The input
% record may be in any of the formats readable by the WFDB library, and it may
% be anywhere in the WFDB path (in a local directory or on a remote web or ftp
% server). The output of 'wabp' is an annotation file named RECORD.wabp (where
% RECORD is replaced by the name of the input record). Within the output
% annotation file, the time of each NORMAL annotation marks an ABP pulse wave
% onset.
%
%
%
% input : data: PPG data
% fs: sampling frequency, default 125 Hz
% from: begin point to analysis
% to : end point to analysis
% output: ppgOnsets: onset position of PPG beats in samples
%
%
%
% CHANGE LOG (should be moved to GitHub as commit messages...)
%
% 03 Aug 2010: by Qiao Li
% 1) sample() function sometimes get WFDB_INVALID_SAMPLE value even when data is good.
% 2) Changed to mysample(), using isigsettime() and getvec() instead, but slow!!!
% 3) Add a mysetbuf() function, read the data to a databuf first, then mysample()
% get data from the buf. It's much more fast than before.
%
%
% 04 Jul 2011 by Qiao Li
% 1) Set eye-closing period for PPG 0.34s, slope width 0.17s
% 2) Remove physical units to ADC units transform //Tm = physadu((unsigned)sig, Tm);
% 3) Add maxmin_2_3_threshold to modify the logic of eye-closing in order to minimize
% the double beats
% 4) Change t += EyeClosing; to t = tpq+EyeClosing;
%
%
% 19 Jul 2011 by Qiao Li
%
% 1) add: (before reading data,at line 480)
% isigsettime(from);
% dataL=from;
% to read data from 'from' setting
% 2) Changed: (after learning period, at line 544)
% (void)sample(sig, tpq);
% if (sample_valid() == 0) break;
% to:
% if (dataend) break;
%
% 18 Oct 2016 by Qiao Li
% 1) add: input parameter fs for different sampling frequency data
% 2) add: re-scale data to ~ +/- 2000
% 3) add: find valley from the original data around 0.25s of tpq
%
% 03 Mar 2017 by Adriana Vest
% Changed name of function to qppg to avoid confusion with wabp
% Previous name: wabp_pleth_new.m
%
% 12 Sep 2018 by Giulia Da Poian
% Changed output variable name to ppgOnsets
%
if nargin<3
from=1;
to=length(data);
end
if nargin<2
fs=125;
end
global BUFLN ebuf lbuf tt_2 aet SLPwindow
ppgOnsets=[];
beat_n=1;
sps=fs; % Sampling Frequency
BUFLN = 4096; % /* must be a power of 2, see slpsamp() */
EYE_CLS = 0.34; % /* eye-closing period is set to 0.34 sec (340 ms) for PPG */
LPERIOD = sps*8; % /* learning period is the first LPERIOD samples */
SLPW = 0.17; % /* Slope width (170ms) for PPG */
NDP = 2.5; % /* adjust threshold if no pulse found in NDP seconds */
TmDEF = 5; % /* minimum threshold value (default) */
Tm = TmDEF;
BUFLN2 = (BUFLN*2);
INVALID_DATA=-32768;
if data(1)<=INVALID_DATA+10
data(1)=mean(data);
end
inv=find(data<=INVALID_DATA+10);
for i=1:length(inv)
data(inv(i))=data(inv(i)-1);
end
% re-scale data to ~ +/- 2000
if length(data)<5*60*sps
data=(data-min(data))./(max(data)-min(data)).*4000-2000;
else
% find max/min every 5 minute for re-scaling data
n=1;
for i=1:5*60*sps:length(data)
max_data(n)=max(data(i:min(i+5*60*sps-1,length(data))));
min_data(n)=min(data(i:min(i+5*60*sps-1,length(data))));
n=n+1;
end
data=(data-median(min_data))./(median(max_data)-median(min_data)).*4000-2000;
end
samplingInterval = 1000.0/sps;
spm = 60 * sps;
EyeClosing = round(sps * EYE_CLS); % /* set eye-closing period */
ExpectPeriod = round(sps * NDP); % /* maximum expected RR interval */
SLPwindow = round(sps * SLPW); % /* slope window size */
timer=0;
ebuf(1:BUFLN)=0;
lbuf=ebuf;
if from>BUFLN
tt_2=from-BUFLN;
else
tt_2=0;
end
aet=0;
t1=8*sps;
t1 = t1+from;
T0 = 0;
n=0;
for t = from:t1
temp = slpsamp(t,data);
if temp > INVALID_DATA+10
T0 = T0+temp;
n=n+1;
end
end
T0 = T0/n; % T0=T0/(t1-from);
Ta = 3 * T0;
learning=1;
t=from;
% /* Main loop */
t = from;
while t <= to
if (learning)
if (t > from + LPERIOD)
learning = 0;
T1 = T0;
t = from; % /* start over */
else
T1 = 2*T0;
end
end
temp = slpsamp(t,data);
if (temp > T1) % /* found a possible ABP pulse near t */
timer = 0;
% /* used for counting the time after previous ABP pulse */
maxd = temp;
mind = maxd;
tmax=t;
for (tt = t + 1: t + EyeClosing-1)
temp2=slpsamp(tt,data);
if temp2 > maxd
maxd=temp2;
tmax=tt;
end
end
if (maxd == temp)
t=t+1;
continue;
end
for (tt = tmax :-1: t - EyeClosing / 2 +1)
temp2=slpsamp(tt,data);
if temp2< mind
mind=temp2;
end
end
if maxd>mind+10
onset=(maxd-mind)/100+2;
tpq=t-round(0.04*fs);
maxmin_2_3_threshold=(maxd-mind)*2.0/3;
for tt=tmax:-1:t-EyeClosing/2+1
temp2=slpsamp(tt,data);
if temp2<maxmin_2_3_threshold
break;
end
end
for tt=tt:-1:t - EyeClosing / 2 + round(0.024*fs)
temp2=slpsamp(tt,data);
temp3=slpsamp(tt-round(0.024*fs),data);
if temp2-temp3<onset
tpq=tt-round(0.016*fs);
break;
end
end
% find valley from the original data around 0.25s of tpq
valley_v = round(tpq);
for valley_i=round(max(2,tpq-round(0.20*fs))):round(min(tpq+round(0.05*fs),length(data)-1))
% If vally is too low, it cannot serve as an index, so move to the next time.
if valley_v <= 0
t = t + 1;
continue;
end
if data(valley_v)>data(valley_i) && data(valley_i)<=data(valley_i-1) && data(valley_i)<=data(valley_i+1)
valley_v=valley_i;
end
end
if (~learning)
% If we are looking for the first peak
if beat_n == 1
% If the proposed peak index > 0
if round(valley_v) > 0
ppgOnsets(beat_n) = round(valley_v);
beat_n = beat_n + 1;
end
else
% Check if rounded valley_v is greater than the prior beat index
if round(valley_v) > ppgOnsets(beat_n-1)
ppgOnsets(beat_n) = round(valley_v);
beat_n = beat_n + 1;
end
end
end
% /* Adjust thresholds */
Ta = Ta + (maxd - Ta)/10;
T1 = Ta / 3;
% /* Lock out further detections during the eye-closing period */
t = tpq+EyeClosing;
end
else
if (~learning)
% /* Once past the learning period, decrease threshold if no pulse
% was detected recently. */
timer = timer+1;
if (timer > ExpectPeriod && Ta > Tm)
Ta=Ta-1;
T1 = Ta / 3;
end
end
end
t=t+1;
end
% Discard first beat because algorithm always finds first minimum value, so trace-back logic
% will find a fir
end
function [beat1] = slpsamp(t,data)
global BUFLN ebuf lbuf tt_2 aet SLPwindow
while (t > tt_2)
prevVal=0;
if (tt_2>0) && (tt_2-1>0) && (tt_2<length(data)) && (tt_2-1<length(data))
val2=data(tt_2 - 1);
val1=data(tt_2);
else
val2=prevVal;
val1=val2;
end
prevVal=val2;
dy = val1-val2;
if (dy < 0)
dy = 0;
end
tt_2=tt_2+1;
M=round(mod(tt_2,(BUFLN-1))+1);
et=dy;
ebuf(M)=et;
% M2=round(mod(tt_2-SLPwindow,(BUFLN-1))+1);
% aet=aet+et-ebuf(M2);
aet=0;
for i=0:SLPwindow-1
p=M-i;
if p<=0
p=p+BUFLN;
end
aet=aet+ebuf(p);
end
lbuf(M) = aet;
end
M3=round(mod(t,(BUFLN-1))+1);
beat1=lbuf(M3);
end