function [fetal_QRSAnn_est,QT_Interval] = physionet2013(tm,ECG)
%% This algorithm for Physionet/CinC competition 2013. Entry 3 Mother PCA
%
% % [fetal_QRSAnn_est,QT_Interval] = physionet2013(tm,ECG) where the inputs and outputs are specified
% below.
% inputs:
% ECG: 4x60000 (4 channels and 1min of signal at 1000Hz) matrix of
% abdominal ECG channels.
% tm : Nx1 vector of time in milliseconds
% output:
% fetal_QRSAnn_est: FQRS Annotations each value indicates the position of
% one of the FQRS detected by the algorithm.
% QT_Interval: 1x1 estimated fetal QT duration
%
% Modified By: Aruna Deogire, MET's Institute of Engineering,Nashik,India
% email - (arunadeogire@gmail.com)
% Last updated: August 24th, 2013 by Aruna Deogire
% ---- check size of ECG ----
if size(ECG,2)>size(ECG,1)
ECG = ECG';
end
% Remove NaN
A=ECG(:,1);
A(isnan(A))=0;
ECG(:,1)=A;
B=ECG(:,2);
B(isnan(B))=0;
ECG(:,2)=B;
C=ECG(:,3);
C(isnan(C))=0;
ECG(:,3)=C;
D=ECG(:,4);
D(isnan(D))=0;
ECG(:,4)=D;
% Variable Initialization
% *************************************************************************
Smooth_Period=149; wav_typ='db6'; level=7;
% *
fs = 1000; % sampling frequency
N = size(ECG,2); % number of abdominal channels
debug = 0; % enter debug mode?
% ---- preprocessing ----
[FilteredECG] = preprocessing(ECG,fs);
% ---- PCA of Mother ECG----
Y=FilteredECG; Y=Y(1:length(Y),:);[COEFF,SCORE] = princomp(Y);Y1 = SCORE(:,1);
% ---- Fetal QRS Detection----
e1=Y1; MQRS=PeakDetection(Y1,1/fs);Mpoint=e1(MQRS);
% e=e1;R_Wave_fECG;MQRS=Rindex;Mpoint=e(MQRS); % Rwave detection by Rpeak Algo
% ---- MECGcancellation----
FECG1 = MECGcancellation(MQRS,Y1',fs,20);
% ---- Post PRocessing ----
R1=smooth(FECG1,Smooth_Period);FECG12=FECG1'-R1; % Postprocessing
% ---- Fetal QRS Detection----
FQRS1=PeakDetection(FECG12,2/fs);f1=FECG12(FQRS1); FQRS=FQRS1';
% [Fpoint FQRS] = Rpeak(FECG12,fs);
S = FECG12;
% QT Point Detections
% Q Point Detection
%*************************************************************************
LQ = length(FQRS);
stepq=fs*0.02; % interval to search Q
for i=2:LQ-1
j=FQRS(i);
[Q,tq]=min(S(j-stepq:j));
j=j-stepq+tq-1;
Qindex(i-1)=j;
Qpoint(i-1)=S(j);
end
% Plot ECG signal with QRS onset marked
% figure;
% plot(S), hold on, plot(FQRS,Fpoint,'r.',Qindex,Qpoint,'k.'),xlim([10000 15000]);grid on; hold off;
% _________________________________________________________________________
% S Point Detection
%*************************************************************************
LS = length(FQRS);
steps=fs*0.02; % interval to search Q
for i=2:LS-1
j=FQRS(i);
[Q,ts]=min(S(j:j+steps));
j=j+ts;
Sindex(i)=j;
Spoint(i)=S(j);
end
% Plot ECG signal with QRS onset marked
% figure;
% plot(S), hold on, plot(FQRS,Fpoint,'r.',Qindex,Qpoint,'k.',Sindex,Spoint,'k.'),xlim([20000 30000]);grid on; hold off;
% _________________________________________________________________________
% T Point Detection
%*************************************************************************
LT = length(Sindex);
stept=fs*0.02; % interval to search T
for i=2:LT-1
j=Sindex(i);
[Q,tt]=max(S(j:j+stept));
j=j+tt;
Tindex(i)=j;
Tpoint(i)=S(j);
end
% T End Detection
%*************************************************************************
LTe = length(Sindex);
% for i=2:LTe-1
% j=Tindex(i);
% while 1
% j=j+1;
% a=S(j+1)-S(j);
% b=S(j)-S(j-1);
% if a>=0 & b<0
% Tendpoint(i)=S(j);
% Tendindex(i)=j;
% break;
% end
% end
% end
stepte=fs*0.01; % interval to search T
for i=2:LTe-1
j=Tindex(i);
[Q,tte]=min(S(j:j+stepte));
j=j+tte;
Tendindex(i)=j;
Tendpoint(i)=S(j);
end
QT = Qindex - Tendindex;
QT_Interval = median(QT);
%__________________________________________________________________________
%__________________________________________________________________________
if debug
m = length(SelectedResidual);
plot(tm,FilteredECG(:,1),'LineWidth',2);
hold on, plot(tm,SelectedResidual,'r',...
tm(FQRS),SelectedResidual(FQRS),'+r',...
tm,FilteredECG(:,ChannelNb)-SelectedResidual,'--k','LineWidth',2);
title('Extracted FECG and detected FQRS');
xlabel('Time (sec)'); ylabel('Amplitude (NU)');
end
fetal_QRSAnn_est = round(1000*FQRS'/fs);
% QT_Interval = 0;
end
function [FilteredECG] = preprocessing(ECG,fs)
% Variable Initialization
% *************************************************************************
fs=1000;Smooth_Period=149; wav_typ='db6'; level=7;
% *************************************************************************
% Filter and BW removal Input Signal
% *************************************************************************
[c,l]=wavedec(ECG(:,1),level,wav_typ); AD1 = wden(c,l,'minimaxi','s','sln',level,wav_typ);
Pattern=smooth(AD1,Smooth_Period);AF1= AD1-Pattern;
[c,l]=wavedec(ECG(:,2),level,wav_typ); AD2 = wden(c,l,'minimaxi','s','sln',level,wav_typ);
Pattern=smooth(AD2,Smooth_Period);AF2= AD2-Pattern;
[c,l]=wavedec(ECG(:,3),level,wav_typ); AD3 = wden(c,l,'minimaxi','s','sln',level,wav_typ);
Pattern=smooth(AD3,Smooth_Period);AF3= AD3-Pattern;
[c,l]=wavedec(ECG(:,4),level,wav_typ); AD4 = wden(c,l,'minimaxi','s','sln',level,wav_typ);
Pattern=smooth(AD4,Smooth_Period);AF4= AD4-Pattern;
FilteredECG=[AF1 AF2 AF3 AF4]; %Vector of Filtered Signals
% *************************************************************************
% FilteredECG = ECG;
end
function residual = MECGcancellation(peaks,ECG,fs,nbCycles)
% MECG cancellation algorithm inspired from [1].
%
% inputs:
% fs: sampling frequency
% nbCycles: number of cycles on which to build the mean MECG template
% ECG: matrix of abdominal ECG channels.
% peaks: MQRS markers in seconds. Each marker corresponds to the
% position of a MQRS.
%
% output:
% residual: residual containing the FECG.
%
% Author: Joachim Behar - IPMG Oxford (joachim.behar@eng.ox.ac.uk)
% Last updated: 03_02_2013
%
% [1] Martens S et al. A robust fetal ECG detection method for
% abdominal recordings. Physiol. Meas. (2007) 28(4) 373�388
% ---- constants ----
r = nbCycles;
ECG_last_r_cycles = zeros(0.7*fs,r);
Pstart = 0.25*fs-1;
Tstop = 0.45*fs;
N = length(peaks); % number of MECG QRS
ECG_temp = zeros(1,length(ECG));
% ---- ECG template ----
for i=1:r
peak_nb = peaks(i+1); % +1 to unsure full cycles
ECG_last_r_cycles(:,i) = ECG(peak_nb-Pstart:peak_nb+Tstop)';
end
ECG_mean = mean(ECG_last_r_cycles,2);
% ---- MECG cancellation ----
for i=1:N
if peaks(i)>Pstart && length(ECG)-peaks(i)>Tstop
M = zeros (0.7*fs,3);
M(1:0.2*fs,1) = ECG_mean(1:Pstart-0.05*fs+1);
M(0.2*fs+1:0.3*fs,2) = ECG_mean(Pstart-0.05*fs+2:Pstart+0.05*fs+1);
M(0.3*fs+1:end,3) = ECG_mean(Pstart+2+0.05*fs:Pstart+1+Tstop);
a = (M'*M)\M'*ECG(peaks(i)-Pstart:peaks(i)+Tstop)';
ECG_temp(peaks(i)-Pstart:peaks(i)+Tstop) = a(1)*M(:,1)'+a(2)*M(:,2)'+a(3)*M(:,3)';
end
end
% compute residual
residual = ECG - ECG_temp;
end
% function [SelectedResidual,ChannelNb] = ChannelSelectionOrCombination(FECG)
% % This function is used to select one of the four abdominal channels
% % that are available or to combine information from these channels
% % (e.g. using PCA) before FQRS detection
% ChannelNb = 1;
% SelectedResidual = FECG(:,ChannelNb); % channel 1 is arbitrarily selected here
% end
%
% function FECG = ResidualPostProcessing(FECG)
% % if postprocessing is performed on the residuals.
% end
%
function peaks = PeakDetection(x,ff,varargin)
%
% peaks = PeakDetection(x,f,flag),
% R-peak detector based on max search
%
% inputs:
% x: vector of input data
% f: approximate ECG beat-rate in Hertz, normalized by the sampling frequency
% flag: search for positive (flag=1) or negative (flag=0) peaks. By default
% the maximum absolute value of the signal, determines the peak sign.
%
% output:
% peaks: vector of R-peak impulse train
%
% Notes:
% - The R-peaks are found from a peak search in windows of length N; where
% N corresponds to the R-peak period calculated from the given f. R-peaks
% with periods smaller than N/2 or greater than N are not detected.
% - The signal baseline wander is recommended to be removed before the
% R-peak detection
%
%
% Open Source ECG Toolbox, version 1.0, November 2006
% Released under the GNU General Public License
% Copyright (C) 2006 Reza Sameni
% Sharif University of Technology, Tehran, Iran -- GIPSA-Lab, INPG, Grenoble, France
% reza.sameni@gmail.com
% Last modified 03_02_2013: Joachim Behar, IPMG Oxford.
% 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.
N = length(x);
peaks = zeros(1,N);
th = .5;
rng = floor(th/ff);
if(nargin==3),
flag = varargin{1};
else
flag = abs(max(x))>abs(min(x));
end
if(flag)
for j = 1:N,
% index = max(j-rng,1):min(j+rng,N);
if(j>rng && j<N-rng)
index = j-rng:j+rng;
elseif(j>rng)
index = N-2*rng:N;
else
index = 1:2*rng;
end
if(max(x(index))==x(j))
peaks(j) = 1;
end
end
else
for j = 1:N,
% index = max(j-rng,1):min(j+rng,N);
if(j>rng && j<N-rng)
index = j-rng:j+rng;
elseif(j>rng)
index = N-2*rng:N;
else
index = 1:2*rng;
end
if(min(x(index))==x(j))
peaks(j) = 1;
end
end
end
% remove fake peaks
I = find(peaks);
d = diff(I);
% z = find(d<rng);
peaks(I(d<rng))=0;
peaks = find(peaks);
end
function [Rpoint Rindex] = Rpeak(e,fs)
% Function to detect Rpeaks
% inputs:
% fs: sampling frequency
% e: Signal Whose Peaks to be Detected
%
%
% output:
% Rpoint: Values of Peaks.
% Rindex: Position of Peaks.
% Author: Aruna Deogire
% Last updated: 17_05_2013
%
L=length(e);
e1=abs(e); % e1 = absolute value of signal
emax=max(e1); % emax = maximum value of e1
eavg =mean(e1);
if emax>= 20*eavg
for i=1:L
if e1(i)>= 10*eavg
% e1(i)=(eavg*5);
e1(i)=0;
end
i=i+1;
end
disp('high peak criteria')
Thd1 =eavg*3
% Thd1 =(mean(e1)/4)*10
e2=e1.*(e1>=Thd1);
% figure;subplot(211),plot(e1,'r') ; subplot(212),plot(e2,'k')
else
Thd2 =(mean(e1)/2.5)*10;
e2=e1.*(e1>=Thd2);
disp('Normal');
end
step=fs*.20; % interval to search R peak
i=1; j=1;
while i<=L-1
if e2(i)~=0
[Rpoint(j),Rindex(j)]=max(e1(i:(i+step)*((i+step)<=(L-1))+(L-1)*((i+step)>(L-1))));
Rindex(j)=Rindex(j)+i-1;
j=j+1; i=i+step;
end
i=i+1;
end
Rpoint=e(Rindex); % [Rpoint, Rindex] = value and position of R peak
end