function [fetal_QRSAnn_est,QT_Interval] = physionet2013(tm,ECG)
% Template algorithm for Physionet/CinC competition 2013. This function can
% be used for events 1 and 2. Participants are free to modify any
% components of the code. However the function prototype must stay the
% same:
%
% [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:
% FQRS: FQRS markers in seconds. Each marker indicates the position of one
% of the FQRS detected by the algorithm.
% QT_Interval: 1x1 estimated fetal QT duration (enter NaN or 0 if you do wish to calculate)
%
%
% Author: Joachim Behar - IPMG Oxford (joachim.behar@eng.ox.ac.uk)
% Last updated: 2. 9. 2013, Jakub Kuzilek (jakub.kuzilek@gmail.com)
% load test.mat
addpath(fullfile(pwd,'QRS_detection'));
% ---- check size of ECG ----
if size(ECG,2)>size(ECG,1)
ECG = ECG';
end
fs = 1000; % sampling frequency
N = size(ECG,2); % number of abdominal channels
debug = 0; % enter debug mode?
% ---- preprocessing ----
[FilteredECG] = preprocessing(ECG,fs);
% MQRS = PeakDetection(FilteredECG(:,1),1/fs);
[~,indx] = sort(kurtosis(FilteredECG));
MQRS = QRSdetection(FilteredECG(:,sort(indx(1:2))),fs,0);
% ---- MECG cancellation ----
for i=1:N % run algorithm for each channel
FECG(:,i) = MECGcancellation(MQRS,FilteredECG(:,i)',fs,20,0); % 5
end
% ---- FQRS detection ----
FQRS = {};
stdfqrs = [];
fqrsnum = [];
for m = 1:N
SelectedResidual = FECG(:,m);
FQRS{end+1} = PeakDetection(SelectedResidual,2/fs);
stdfqrs(end+1) = std(diff(FQRS{end}));
fqrsnum(end+1) = length(FQRS{end});
FQRS{end+1} = correctFQRS(SelectedResidual,FQRS{end});
stdfqrs(end+1) = std(diff(FQRS{end}));
fqrsnum(end+1) = length(FQRS{end});
FQRS{end+1} = findFQRS(SelectedResidual);
stdfqrs(end+1) = std(diff(FQRS{end}));
fqrsnum(end+1) = length(FQRS{end});
FQRS{end+1} = correctFQRS(SelectedResidual,FQRS{end});
stdfqrs(end+1) = std(diff(FQRS{end}));
fqrsnum(end+1) = length(FQRS{end});
end
FQRS(fqrsnum < 20) = [];
stdfqrs(fqrsnum < 20) = [];
fqrsnum(fqrsnum < 20) = [];
[v, lok] = min(stdfqrs);
FQRS = FQRS{lok};
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;
rmpath(fullfile(pwd,'QRS_detection'));
end
function [FilteredECG] = preprocessing(ECG,fs)
% ---- preprocess the data ----
time = 1:length(ECG);
for m = 1:min(size(ECG))
if any(isnan(ECG(:,m)))
ECG(:,m) = pchip(time(~isnan(ECG(:,2))),ECG(~isnan(ECG(:,2)),2),time);
end
end
FilteredECG = ECG;
for m = 1:size(ECG,2)
FilteredECG(:,m) = filterIsoline(ECG(:,m),fs);
end
aa = filter(ones(1,50)/50,1,[FilteredECG; zeros(25,size(ECG,2))]);
FilteredECG = FilteredECG - aa(26:end,:);
end
function residual = MECGcancellation(peaks,ECG,fs,nbCycles, rl)
% 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: 2. 9. 2013, Jakub Kuzilek (jakub.kuzilek@gmail.com)
%
% [1] Martens S et al. A robust fetal ECG detection method for
% abdominal recordings. Physiol. Meas. (2007) 28(4) 373�388
% ---- constants ----
r = nbCycles;
Pstart = 0.25*fs-1;
Tstop = 0.45*fs;
N = length(peaks); % number of MECG QRS
ECG_temp = zeros(1,length(ECG));
% ---- ECG template ----
if mod(N,r)
iters = floor(N/r)+1;
else
iters = floor(N/r);
end
for m = 0:iters
ECG_last_r_cycles = zeros(0.7*fs,r);
ECG_mean = zeros(0.7*fs,1);
cnt = 1;
for i=m*r+1:min([m*r+r N])
if peaks(i)>Pstart && length(ECG)-peaks(i)>Tstop && (i<N && peaks(i+1)-peaks(i) > Tstop + 50)
ECG_last_r_cycles(:,cnt) = ECG(peaks(i)-Pstart:peaks(i)+Tstop)';
elseif peaks(i)<=Pstart
ECG_last_r_cycles(:,cnt) = [zeros(1,Pstart-peaks(i)+1), ECG(1:peaks(i)+Tstop)]';
elseif i == N && length(ECG)-peaks(i)<Tstop
ECG_last_r_cycles(:,cnt) = [ECG(peaks(i)-Pstart:end), zeros(1,Tstop+peaks(i)-length(ECG))]';
elseif (i<N && peaks(i+1)-peaks(i) < Tstop + 50)
lengthReduction = Tstop - peaks(i+1) + peaks(i)+50;
if lengthReduction < 50
lengthReduction = 50;
end
ECG_last_r_cycles(:,cnt) = [ ECG(peaks(i)-Pstart:peaks(i)+Tstop-lengthReduction) zeros(1, lengthReduction)]';
end
cnt = cnt+1;
end
ECG_mean =mean(ECG_last_r_cycles,2);
% ---- MECG cancellation ----
for i= m*r+1:min([m*r+r N])%1:N
if peaks(i)>Pstart && length(ECG)-peaks(i)>Tstop && (i<N && peaks(i+1)-peaks(i) > Tstop + 50)
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);
out = bestFit(peaks(i), ECG, M(:,1)'+M(:,2)'+M(:,3)', Pstart, Tstop);
if out-Pstart<1
out = peaks(i);
end
a = (M'*M)\M'*ECG(out-Pstart:out+Tstop)';
ECG_temp(out-Pstart:out+Tstop) = a(1)*M(:,1)'+a(2)*M(:,2)'+a(3)*M(:,3)';
elseif peaks(i)<=Pstart
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);
out = bestFit(peaks(i), ECG, M(:,1)'+M(:,2)'+M(:,3)', Pstart, Tstop);
if Pstart < out
template = ECG(out-Pstart:out+Tstop);
a = (M'*M)\M'*template';
ECG_temp(out-Pstart:out+Tstop) = a(1)*M(:,1)'+a(2)*M(:,2)'+a(3)*M(:,3)';
else
template = [zeros(1,Pstart-out+1), ECG(1:out+Tstop)];
a = (M'*M)\M'*template';
ECG_temp(1:out+Tstop) = a(1)*M(Pstart-out+2:end,1)'+a(2)*M(Pstart-out+2:end,2)'+a(3)*M(Pstart-out+2:end,3)';
end
elseif (i<N && peaks(i)-peaks(i+1) < Tstop + 50)
lengthReduction = Tstop - peaks(i+1) + peaks(i)+50;
if lengthReduction < 50
lengthReduction = 50;
end
M = zeros (0.7*fs-lengthReduction,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-lengthReduction);
out = bestFit(peaks(i), ECG, M(:,1)'+M(:,2)'+M(:,3)', Pstart, Tstop-lengthReduction);
if Pstart < out
template = ECG(out-Pstart:out+Tstop-lengthReduction);
a = (M'*M)\M'*template';
ECG_temp(out-Pstart:out+Tstop-lengthReduction) = a(1)*M(:,1)'+a(2)*M(:,2)'+a(3)*M(:,3)';
else
template = [zeros(1,Pstart-out+1), ECG(1:out+Tstop-lengthReduction)];
a = (M'*M)\M'*template';
ECG_temp(1:out+Tstop-lengthReduction) = a(1)*M(Pstart-out+2:end,1)'+a(2)*M(Pstart-out+2:end,2)'+a(3)*M(Pstart-out+2:end,3)';
end
end
end
end
% compute residual
residual = ECG - ECG_temp;
x = 0;
for m = 1:length(peaks)
x = x + sum(residual(max([peaks(m)-Pstart 1]):min([peaks(m)+Tstop length(residual)])).^2)/700;
end
x = x/length(peaks);
if x > 15 && rl < 100
rl = rl+1;
residual = MECGcancellation(peaks,residual,fs,20,rl);
end
end
function out = bestFit(peak, ECG, template, Pstart, Tstop)
err = zeros(1,101);
for m = peak-50:peak+50
if m-Pstart<1
err(m-peak+51) = ([zeros(1, Pstart-m+1), ECG(1:m+Tstop)]-template)*([zeros(1, Pstart-m+1), ECG(1:m+Tstop)]-template)';
else
err(m-peak+51) = (ECG(m-Pstart:m+Tstop)-template)*(ECG(m-Pstart:m+Tstop)-template)';
end
end
[v, pos] = min(err);
out = peak-51+pos;
end
function out = computeECGMEAN(ECG, fs, r, Tstop, Pstart,peaks)
ECG_last_r_cycles = zeros(0.7*fs,r);
for i=1:r
peak_nb = peaks(i+1);
ECG_last_r_cycles(:,i) = ECG(peak_nb-Pstart:peak_nb+Tstop)';
end
out = mean(ECG_last_r_cycles,2);
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)
for m = 1:size(FECG,2)
for n = 30:35
FECG(:,m) = adaptiveANC(FECG(:,m),1000,n);
end
end
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