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ecgsyn-1.0.0/Matlab/HEADER.shtml
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ecgsyn-1.0.0/Matlab/HEADER.shtml
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<!--#set var="TITLE" value="ECGSYN for Matlab/Octave"-->
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<!--#include virtual="/head.shtml"-->
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<p>
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This directory contains <a href="../">ECGSYN</a> implemented in Matlab
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m-code.
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<hr>
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52
ecgsyn-1.0.0/Matlab/derivsecgsyn.m
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ecgsyn-1.0.0/Matlab/derivsecgsyn.m
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function dxdt = derivsecgsyn(t,x,flag,rr,sfint,ti,ai,bi)
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% dxdt = derivsecgsyn(t,x,flag,rr,sampfreq,ti,ai,bi)
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% ODE file for generating the synthetic ECG
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% This file provides dxdt = F(t,x) taking input paramters:
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% rr: rr process
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% sfint: Internal sampling frequency [Hertz]
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% Order of extrema: [P Q R S T]
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% ti = angles of extrema [radians]
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% ai = z-position of extrema
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% bi = Gaussian width of peaks
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% Copyright (c) 2003 by Patrick McSharry & Gari Clifford, All Rights Reserved
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% See IEEE Transactions On Biomedical Engineering, 50(3), 289-294, March 2003.
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% Contact P. McSharry (patrick AT mcsharry DOT net) or
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% G.D. Clifford (gari AT mit DOT edu)
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% This program is free software; you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as published by
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% the Free Software Foundation; either version 2 of the License, or
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% (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License
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% along with this program; if not, write to the Free Software
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% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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%
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% ecgsyn.m and its dependents are freely availble from Physionet -
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% http://www.physionet.org/ - please report any bugs to the authors above.
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xi = cos(ti);
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yi = sin(ti);
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ta = atan2(x(2),x(1));
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r0 = 1;
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a0 = 1.0 - sqrt(x(1)^2 + x(2)^2)/r0;
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ip = 1+floor(t*sfint);
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w0 = 2*pi/rr(ip);
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fresp = 0.25;
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zbase = 0.005*sin(2*pi*fresp*t);
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dx1dt = a0*x(1) - w0*x(2);
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dx2dt = a0*x(2) + w0*x(1);
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dti = rem(ta - ti, 2*pi);
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dx3dt = - sum(ai.*dti.*exp(-0.5*(dti./bi).^2)) - 1.0*(x(3) - zbase);
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dxdt = [dx1dt; dx2dt; dx3dt];
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ecgsyn-1.0.0/Matlab/ecgsyn.m
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ecgsyn-1.0.0/Matlab/ecgsyn.m
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function [s, ipeaks] = ecgsyn(sfecg,N,Anoise,hrmean,hrstd,lfhfratio,sfint,ti,ai,bi)
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% [s, ipeaks] = ecgsyn(sfecg,N,Anoise,hrmean,hrstd,lfhfratio,sfint,ti,ai,bi)
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% Produces synthetic ECG with the following outputs:
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% s: ECG (mV)
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% ipeaks: labels for PQRST peaks: P(1), Q(2), R(3), S(4), T(5)
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% A zero lablel is output otherwise ... use R=find(ipeaks==3);
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% to find the R peaks s(R), etc.
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%
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% Operation uses the following parameters (default values in []s):
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% sfecg: ECG sampling frequency [256 Hertz]
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% N: approximate number of heart beats [256]
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% Anoise: Additive uniformly distributed measurement noise [0 mV]
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% hrmean: Mean heart rate [60 beats per minute]
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% hrstd: Standard deviation of heart rate [1 beat per minute]
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% lfhfratio: LF/HF ratio [0.5]
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% sfint: Internal sampling frequency [256 Hertz]
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% Order of extrema: [P Q R S T]
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% ti = angles of extrema [-70 -15 0 15 100] degrees
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% ai = z-position of extrema [1.2 -5 30 -7.5 0.75]
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% bi = Gaussian width of peaks [0.25 0.1 0.1 0.1 0.4]
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% Copyright (c) 2003 by Patrick McSharry & Gari Clifford, All Rights Reserved
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% See IEEE Transactions On Biomedical Engineering, 50(3), 289-294, March 2003.
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% Contact P. McSharry (patrick@mcsharry.net) or G. Clifford (gari@mit.edu)
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% This program is free software; you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as published by
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% the Free Software Foundation; either version 2 of the License, or
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% (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License
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% along with this program; if not, write to the Free Software
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% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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%
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% ecgsyn.m and its dependents are freely availble from Physionet -
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% http://www.physionet.org/ - please report any bugs to the authors above.
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% set parameter default values
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if nargin < 1
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sfecg = 256;
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end
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if nargin < 2
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N = 256;
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end
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if nargin < 3
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Anoise = 0;
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end
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if nargin < 4
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hrmean = 60;
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end
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if nargin < 5
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hrstd = 1;
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end
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if nargin < 6
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lfhfratio = 0.5;
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end
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if nargin < 7
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sfint = 512;
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end
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if nargin <8
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% P Q R S T
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ti = [-70 -15 0 15 100];
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end
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% convert to radians
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ti = ti*pi/180;
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if nargin <9 % z position of attractor
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% P Q R S T
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ai = [1.2 -5 30 -7.5 0.75];
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end
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if nargin <10 % Gaussian width of each attractor
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% P Q R S T
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bi = [0.25 0.1 0.1 0.1 0.4];
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end
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% adjust extrema parameters for mean heart rate
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hrfact = sqrt(hrmean/60);
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hrfact2 = sqrt(hrfact);
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bi = hrfact*bi;
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ti = [hrfact2 hrfact 1 hrfact hrfact2].*ti;
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% check that sfint is an integer multiple of sfecg
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q = round(sfint/sfecg);
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qd = sfint/sfecg;
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if q ~= qd
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error(['Internal sampling frequency (sfint) must be an integer multiple ' ...
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'of the ECG sampling frequency (sfecg). Your current choices are: ' ...
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'sfecg = ' int2str(sfecg) ' and sfint = ' int2str(sfint) '.']);
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end
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% define frequency parameters for rr process
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% flo and fhi correspond to the Mayer waves and respiratory rate respectively
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flo = 0.1;
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fhi = 0.25;
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flostd = 0.01;
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fhistd = 0.01;
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fid = 1;
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fprintf(fid,'ECG sampled at %d Hz\n',sfecg);
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fprintf(fid,'Approximate number of heart beats: %d\n',N);
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fprintf(fid,'Measurement noise amplitude: %d \n',Anoise);
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fprintf(fid,'Heart rate mean: %d bpm\n',hrmean);
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fprintf(fid,'Heart rate std: %d bpm\n',hrstd);
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fprintf(fid,'LF/HF ratio: %g\n',lfhfratio);
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fprintf(fid,'Internal sampling frequency: %g\n',sfint);
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fprintf(fid,' P Q R S T\n');
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fprintf(fid,'ti = [%g %g %g %g %g] radians\n',ti(1),ti(2),ti(3),ti(4),ti(5));
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fprintf(fid,'ai = [%g %g %g %g %g]\n',ai(1),ai(2),ai(3),ai(4),ai(5));
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fprintf(fid,'bi = [%g %g %g %g %g]\n',bi(1),bi(2),bi(3),bi(4),bi(5));
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% calculate time scales for rr and total output
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sampfreqrr = 1;
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trr = 1/sampfreqrr;
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tstep = 1/sfecg;
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rrmean = (60/hrmean);
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Nrr = 2^(ceil(log2(N*rrmean/trr)));
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% compute rr process
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rr0 = rrprocess(flo,fhi,flostd,fhistd,lfhfratio,hrmean,hrstd,sampfreqrr,Nrr);
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% upsample rr time series from 1 Hz to sfint Hz
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rr = interp(rr0,sfint);
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% make the rrn time series
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dt = 1/sfint;
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rrn = zeros(length(rr),1);
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tecg=0;
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i = 1;
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while i <= length(rr)
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tecg = tecg+rr(i);
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ip = round(tecg/dt);
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rrn(i:ip) = rr(i);
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i = ip+1;
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end
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Nt = ip;
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% integrate system using fourth order Runge-Kutta
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fprintf(fid,'Integrating dynamical system\n');
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x0 = [1,0,0.04];
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Tspan = [0:dt:(Nt-1)*dt];
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[T,X0] = ode45('derivsecgsyn',Tspan,x0,[],rrn,sfint,ti,ai,bi);
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% downsample to required sfecg
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X = X0(1:q:end,:);
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% extract R-peaks times
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ipeaks = detectpeaks(X, ti, sfecg);
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% Scale signal to lie between -0.4 and 1.2 mV
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z = X(:,3);
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zmin = min(z);
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zmax = max(z);
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zrange = zmax - zmin;
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z = (z - zmin)*(1.6)/zrange -0.4;
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% include additive uniformly distributed measurement noise
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eta = 2*rand(length(z),1)-1;
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s = z + Anoise*eta;
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function rr = rrprocess(flo, fhi, flostd, fhistd, lfhfratio, hrmean, hrstd, sfrr, n)
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w1 = 2*pi*flo;
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w2 = 2*pi*fhi;
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c1 = 2*pi*flostd;
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c2 = 2*pi*fhistd;
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sig2 = 1;
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sig1 = lfhfratio;
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rrmean = 60/hrmean;
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rrstd = 60*hrstd/(hrmean*hrmean);
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df = sfrr/n;
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w = [0:n-1]'*2*pi*df;
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dw1 = w-w1;
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dw2 = w-w2;
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Hw1 = sig1*exp(-0.5*(dw1/c1).^2)/sqrt(2*pi*c1^2);
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Hw2 = sig2*exp(-0.5*(dw2/c2).^2)/sqrt(2*pi*c2^2);
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Hw = Hw1 + Hw2;
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Hw0 = [Hw(1:n/2+1); Hw(n/2:-1:2)];
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Sw = (sfrr/2)*sqrt(Hw0);
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ph0 = 2*pi*rand(n/2-1,1);
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ph = [ 0; ph0; 0; -flipud(ph0) ];
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SwC = Sw .* exp(j*ph);
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x = (1/n)*real(ifft(SwC));
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xstd = std(x);
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ratio = rrstd/xstd;
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rr = rrmean + x*ratio;
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function ind = detectpeaks(X, thetap, sfecg)
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N = length(X);
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irpeaks = zeros(N,1);
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theta = atan2(X(:,2),X(:,1));
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ind0 = zeros(N,1);
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for i=1:N-1
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a = ( (theta(i) <= thetap) & (thetap <= theta(i+1)) );
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j = find(a==1);
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if ~isempty(j)
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d1 = thetap(j) - theta(i);
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d2 = theta(i+1) - thetap(j);
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if d1 < d2
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ind0(i) = j;
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else
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ind0(i+1) = j;
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end
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end
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end
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d = ceil(sfecg/64);
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d = max([2 d])
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ind = zeros(N,1);
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z = X(:,3);
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zmin = min(z);
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zmax = max(z);
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zext = [zmin zmax zmin zmax zmin];
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sext = [1 -1 1 -1 1];
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for i=1:5
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clear ind1 Z k vmax imax iext;
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ind1 = find(ind0==i);
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n = length(ind1);
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Z = ones(n,2*d+1)*zext(i)*sext(i);
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for j=-d:d
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k = find( (1 <= ind1+j) & (ind1+j <= N) );
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Z(k,d+j+1) = z(ind1(k)+j)*sext(i);
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end
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[vmax, ivmax] = max(Z,[],2);
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iext = ind1 + ivmax-d-1;
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ind(iext) = i;
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end
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9
ecgsyn-1.0.0/Matlab/index.html
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9
ecgsyn-1.0.0/Matlab/index.html
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<html>
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<head><title>Index of /static/published-projects/ecgsyn/1.0.0/Matlab/</title></head>
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<body>
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<h1>Index of /static/published-projects/ecgsyn/1.0.0/Matlab/</h1><hr><pre><a href="../">../</a>
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<a href="HEADER.shtml">HEADER.shtml</a> 12-Apr-2019 17:35 186
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<a href="derivsecgsyn.m">derivsecgsyn.m</a> 12-Apr-2019 17:35 1911
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<a href="ecgsyn.m">ecgsyn.m</a> 12-Apr-2019 17:35 6795
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</pre><hr></body>
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</html>
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