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Beats.m
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Beats.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% BRAVEHEART - Open source software for electrocardiographic and vectorcardiographic analysis
% Beats.m -- Class for storing beat annotations
% Copyright 2016-2024 Hans F. Stabenau and Jonathan W. Waks
%
% Source code/executables: https://github.com/BIVectors/BRAVEHEART
% Contact: [email protected]
%
% BRAVEHEART 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 3 of the License,
% or (at your option) any later version.
%
% BRAVEHEART 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, see <https://www.gnu.org/licenses/>.
%
% This software is for research purposes only and is not intended to diagnose or treat any disease.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
classdef Beats
% Each instance of the Beats is an annotation of a VCG
% This is stored in the properties as arrays with the same dimension that store the indices of the sample in the VCG
% so if the start of QRS are at sample 100, 200, and 300, while the S waves are at 150, 250, and 350, then you would have
% Q = [100 200 300 ...]
% S = [150 250 350 ...]
% The annotation is computed via calling the constructor with a VCG. Nothing about the VCG itself is stored in this class.
properties (SetAccess=private)
Q
QRS
S
T
Tend
outlier % logical flags for beats: is outlier beat?
pvc % logical flags for beats: is PVC?
nnet_flag % problem with nnet annotation?
nnet_nan % NNet can't find a fiducial point in the median beat
QRS_rem_pvc % List of beats that were removed as PVCs
QRS_rem_outlier % List of beats that were removed as outliers
QRS_rem_manual % List of beats that were manually removed
QRS_rem_bad % List of beats that were removed due to other issues (too close to start/end of recording)
end
methods
function obj = Beats(varargin)
switch nargin
case 5
[Q, QRS, S, T, Tend] = varargin{:};
if length(QRS) == length(Q) && length(QRS) == length(S) && length(QRS) == length(T) && ...
length(QRS) == length(Tend)
obj.QRS = QRS;
obj.Q = Q;
obj.S = S;
obj.T = T;
obj.Tend = Tend;
else
error('Vectors different length in Beats constructor');
end
case 4
[Q, QRS, S, Tend] = varargin{:};
if length(QRS) == length(Q) && length(QRS) == length(S) && ...
length(QRS) == length(Tend)
obj.QRS = QRS;
obj.Q = Q;
obj.S = S;
obj.Tend = Tend;
else
error('Vectors different length in Beats constructor');
end
case 3
[vcg, QRS, aps] = varargin{:};
hz = vcg.hz;
% if aps.debug; figure; plot(vcg.VM); hold on; end
if length(QRS) ~= 1
RR = diff(QRS); RR(end+1) = round(mean(RR));
STendsamp = aps.STendsamp(RR);
else
STendsamp = aps.STend;
end
% If using regular annotation for median reanno
if strcmp(aps.median_reanno_method,'Std') || length(QRS) ~= 1
[obj.Q, obj.QRS, obj.S, obj.T, obj.Tend] = ...
autoMFannotate(vcg.VM, QRS, aps.QRsamp(hz), vcg.endspikes, ...
aps.RSsamp(hz), aps.STstartsamp(hz), STendsamp, aps.Tendstr, ...
aps.autoMF, aps.MF_width_samp(hz), aps.autoMF_thresh, hz, aps.debug);
end
% Add to "bad" beats if anno didnt like a beat too
% close to start or end of the signal (eg they were cut
% off and were only included in the HR calculation).
if length(QRS) > length(obj.QRS) && length(QRS) ~= 1
C = setxor(QRS,obj.QRS);
obj.QRS_rem_bad = vertcat(obj.QRS_rem_bad, C);
% If end up with a 0x1 double vector make this empty
if isempty(obj.QRS_rem_bad)
obj.QRS_rem_bad = [];
end
% Sort in ascending order
obj.QRS_rem_bad = sort(obj.QRS_rem_bad);
end
% If using nnet for median reanno
if strcmp(aps.median_reanno_method,'NNet') && length(QRS) == 1
[obj.Q, obj.S, obj.T, obj.Tend, obj.nnet_flag, obj.nnet_nan] = nnet_median_annotate(vcg, aps.debug);
obj.QRS = QRS;
end
% check for overlapping beats
for i=1:length(obj.QRS)-1
if obj.Tend(i) > obj.Q(i+1); obj.Tend(i) = NaN; end
end
case 0
otherwise
error('Beats:constructor', 'got %d args', nargin);
end
end
function b = septum(obj, vcg, window, aps) %#ok<INUSD>
b.Q = obj.Q;
[~, b.QRS] = findpeaks(vcg.VM, 'NPeaks', 1);
b.Tend = obj.Q+window;
b.S = waveEndPk(vcg.VM, b.QRS, b.Tend);
b.S = b.S + b.Q - 1;
end
function [startb, endb, qonb, qoffb, toffb] = medianloc(obj, vcg, ap)
% given a stack of Q, R, S, and T, compute the indices of the start and end indices which encompass them,
% assuming the QRS complexes are lined up on their peaks or centers of mass
R = com_or_rpeak(obj.QRS, vcg.VM, vcg.hz, ap);
[qonb, toffb, qoffb] = medianloc(obj.Q, R, obj.S, obj.Tend);
startb = qonb + ap.shiftq_samp(vcg.hz);
endb = toffb + ap.shiftt_samp(vcg.hz);
end
function q = qend(obj); q = obj.S-(obj.Q-1); end
function l = length(obj); l = length(obj.QRS); end
function b = beatmatrix(obj); b = [obj.Q obj.QRS obj.S obj.Tend]; end
function b = fixTend(obj, ap)
% Try to salvage beats by guessing Tend when the heuristic annotator failed
N = obj.length();
Tendnan = isnan(obj.Tend);
overlapped = obj.Tend(1:N-1) > obj.Q(2:N); overlapped(N) = false;
badind = Tendnan | overlapped;
bad = badind==1;
b = obj;
rr = obj.RRint();
endw = ap.STend;
%endw = ap.STend*1.5;
%if endw > 75; endw = 75; end
% if the last beat is bad, just delete it
if bad(N); deleteLast = true; else; deleteLast = false; end
bad = bad(1:N-1);
b.Tend(bad) = round(b.S(bad) + rr(bad)*endw/100);
if deleteLast; b = b.delete(N, "bad"); end
end
function obj = find_pvcs(obj, vcg, ap)
% PVC detector, works by computing a cross correlation and RMSE of each beat with the median beat
R = com_or_rpeak(obj.QRS, vcg.VM, vcg.hz, ap);
[~, ~, ~, px, ~] = pvc_stats(ap.pvcthresh, ap.rmse_pvcthresh, ap.keep_pvc, [obj.Q R obj.S obj.Tend], vcg.X);
[~, ~, ~, py, ~] = pvc_stats(ap.pvcthresh, ap.rmse_pvcthresh, ap.keep_pvc, [obj.Q R obj.S obj.Tend], vcg.Y);
[~, ~, ~, pz, ~] = pvc_stats(ap.pvcthresh, ap.rmse_pvcthresh, ap.keep_pvc, [obj.Q R obj.S obj.Tend], vcg.Z);
P = px + py + pz;
P(P<2) = 0;
P(P>=2) = 1;
% % DEBUG CODE TO CALC ACCURACY OF PVC DETECTOR
% % % open your file for writing
% cc=num2cell(double(P),2);
% C=num2str(cc{1});
%
% fid = fopen(strcat('R:\PVC database\__FINAL_PVCS\_', num2str(100*ap.pvcthresh),'_',num2str(10*ap.rmse_pvcthresh),'.csv'),'a+');
% % write the matrix
% if fid > 0
% fprintf(fid,'%s,\n',C');
% fclose(fid);
% end
if ap.keep_pvc == 0
obj.pvc = logical(P);
else
obj.pvc = logical(~P);
end
end
function obj = delete(obj, ind, flag)
% If don't supply a flag it is manual
if nargin == 2 && isnumeric(ind)
flag = 'manual';
end
obj_old = obj;
obj.Q(ind) = [];
obj.QRS(ind) = [];
obj.S(ind) = [];
if ~isempty(obj.T); obj.T(ind) = []; end
obj.Tend(ind) = [];
if ~isempty(obj.outlier); obj.outlier(ind) = []; end
if ~isempty(obj.pvc); obj.pvc(ind) = []; end
% If end up with 0 beats left over dont remove anything!!!
if isempty(obj.Q)
% Reset to prior to deletion
obj = obj_old;
end
% Moved deleted beat to 'deleted' field
if strcmp(flag,"pvc")
obj.QRS_rem_pvc = vertcat(obj.QRS_rem_pvc, obj_old.QRS(ind));
% If end up with a 0x1 double vector make this empty
if isempty(obj.QRS_rem_pvc)
obj.QRS_rem_pvc = [];
end
% Sort in ascending order
obj.QRS_rem_pvc = sort(obj.QRS_rem_pvc);
elseif strcmp(flag,"outlier")
obj.QRS_rem_outlier = vertcat(obj.QRS_rem_outlier, obj_old.QRS(ind));
% If end up with a 0x1 double vector make this empty
if isempty(obj.QRS_rem_outlier)
obj.QRS_rem_outlier = [];
end
% Sort in ascending order
obj.QRS_rem_outlier = sort(obj.QRS_rem_outlier);
elseif strcmp(flag,"bad")
obj.QRS_rem_bad = vertcat(obj.QRS_rem_bad, obj_old.QRS(ind));
% If end up with a 0x1 double vector make this empty
if isempty(obj.QRS_rem_bad)
obj.QRS_rem_bad = [];
end
% Sort in ascending order
obj.QRS_rem_bad = sort(obj.QRS_rem_bad);
else
obj.QRS_rem_manual = vertcat(obj.QRS_rem_manual, obj_old.QRS(ind));
% If end up with a 0x1 double vector make this empty
if isempty(obj.QRS_rem_manual)
obj.QRS_rem_manual = [];
end
% Sort in ascending order
obj.QRS_rem_manual = sort(obj.QRS_rem_manual);
end
end
function obj = change(obj, ind, newbeat)
if length(newbeat) == 4
newQ = newbeat(1);
newQRS = newbeat(2);
newS = newbeat(3);
newTend = newbeat(4);
else
error('New beat is 4 points long - do NOT include Tpeak');
end
obj.Q(ind) = newQ;
obj.QRS(ind) = newQRS;
obj.S(ind) = newS;
% copy over Tpeak
obj.Tend(ind) = newTend;
end
function b = add(obj, newbeat)
if length(newbeat) == 4
newQ = newbeat(1);
newQRS = newbeat(2);
newS = newbeat(3);
newT = 0; % Zero for T since not used
newTend = newbeat(4);
else
error('New beat is 4 points long - do NOT include Tpeak');
end
b = obj;
len = obj.length();
ind = len + 1;
b.Q(ind) = newQ;
b.QRS(ind) = newQRS;
b.S(ind) = newS;
b.T(ind) = newT;
b.Tend(ind) = newTend;
end
function b = shift_q(obj, shift)
b = obj;
b.Q = b.Q+shift;
end
function b = shift_r(obj, shift)
b = obj;
b.QRS = b.QRS+shift;
end
function b = shift_s(obj, shift)
b = obj;
b.S = b.S+shift;
end
function b = shift_t(obj, shift)
b = obj;
b.T = b.T+shift;
end
function b = shift_tend(obj, shift)
b = obj;
b.Tend = b.Tend+shift;
end
function d = QRSdur(obj); d = obj.S-obj.Q; end
function d = RRint(obj); N=obj.length(); d = obj.QRS(2:N) - obj.QRS(1:N-1); end
function obj = find_outliers(obj, vcg, ap)
cutpt = ap.modz_cutoff;
% dynamic cutpt based on number of beats?
length(obj.Q);
[outlier_matrix, ~] = find_outliers([obj.Q obj.QRS obj.S obj.Tend], vcg.VM, vcg.hz, cutpt); % careful! definition of beatmatrix different
o = outlier_matrix(4,:) + outlier_matrix(1,:);
obj.outlier = (o>=1)';
end
function v = cells(obj)
lab = obj.labels();
v = cell(1, length(lab));
for i = 1:length(lab)
v{i} = mat2str(obj.(lab{i})');
T = v{i};
T(T=='[') = [];
T(T==']') = [];
v{i} = T;
end
end
function labels = labels(obj)
labels_long = properties(obj)';
delete_names = [{'T'} {'outlier'} {'pvc'} {'nnet_flag'} {'nnet_nan'}];
for k = 1:length(delete_names)
idx(k) = find(strcmp(labels_long,delete_names{k}));
end
labels_long(idx)=[];
labels = labels_long;
end
end
% default copy, assignment, destructor
end