%
% Median beat calculation code V.1.1
% Erick Andres Perez Alday, PhD, <perezald@ohsu.edu>
% Larisa Tereshchenko, MD, PhD, < tereshch@ohsu.edu >
% Last update: August 1st, 2018
clear
clc
close all
warning('OFF');
%delete(gcp('nocreate'))
% Input:
% 1. sampling frequency in HZ
% 2. matlab file containing the following:
% - XYZ_O(:,3): 10 seconds X, Y, and Z leads
% - Rx: index of R peak on X lead
% - Ry: index of R peak on Y lead
% - Rz: index of R peak on Z lead
% Output:
% 2. Mat file containing the calculated median beat
% 4. 2D jpeg of median VectorMagniute plot
%% =========================== File and user input =============================
% sampling frequency
% sampling frequency
prompt='What is the sampling frequency in Hz';
dlg_title='Sample Frequency';
fs_d = inputdlg(prompt,dlg_title,1);
fs=str2num(fs_d{1});
% load mat files
[file_name,path_name] = uigetfile('*','Select file for Median beat');
%% file import
file_ID = strsplit(file_name,'.');
file_path = fullfile(path_name,file_name);
matfile = matfile(file_path)
%% Create Results folder
Results_folder = [path_name, '/', 'Results', '/'];
if (exist(Results_folder,'file') ~= 7)
mkdir (Results_folder);
end
%% ===================== Initialize variables ========================
XYZ_O=[];
Rpeaks=[];
Beats_x_T=[];
Beats_y_T=[];
Beats_z_T=[];
XYZ_M_T=[];
VecMag_T=[];
%% ===================== load variables from .mat file ========================
XYZ_O=matfile.XYZ_O;
Rpeaks(:,1) = matfile.Rx;
Rpeaks(:,2) = matfile.Ry;
Rpeaks(:,3) = matfile.Rz;
R_no=length(matfile.Rx);
%% Total number of samples
Total_samples=length(XYZ_O(:,1));
%% Length of each beat is set to 1200 ms.
Beat_length=fs*1.2;
% =========================== Variable Calculation ============-================
%% Exclude the first if we do not have a complete first beat
if (Rpeaks(1,1)<(Beat_length/2)) || (Rpeaks(1,2)<(Beat_length/2)) || (Rpeaks(1,3)<(Beat_length/2))
c_int=2;
else
c_int=1;
end
%% Exclude the last if we do not have a complete last beat
if abs(Rpeaks(end-1,1)-Total_samples)<(Beat_length/2) || abs(Rpeaks(end-1,2)-Total_samples)<(Beat_length/2) || abs(Rpeaks(end-1,3)-Total_samples)<(Beat_length/2)
c_fin=2;
else
c_fin=1;
end
%% Separate the each beat in the X, Y, and Z leads. Each beat is centered on the R peak detected on the X lead.
bct=1;
for ii=c_int:R_no-c_fin
Beats_x_T(:,bct)=XYZ_O(Rpeaks(ii,1)-((Beat_length/2)-1):Rpeaks(ii,1)+(Beat_length/2),1);
Beats_y_T(:,bct)=XYZ_O(Rpeaks(ii,1)-((Beat_length/2)-1):Rpeaks(ii,1)+(Beat_length/2),2);
Beats_z_T(:,bct)=XYZ_O(Rpeaks(ii,1)-((Beat_length/2)-1):Rpeaks(ii,1)+(Beat_length/2),3);
bct=bct+1;
end
%% Create the median beat of each X, Y, and Z leads
XYZ_M_T(:,1)=median(Beats_x_T');
XYZ_M_T(:,2)=median(Beats_y_T');
XYZ_M_T(:,3)=median(Beats_z_T');
%% Calculate the Vector Magnitude (Euclidean norm)
for ii=1:length(XYZ_M_T(:,1))
VecMag_T(ii)=norm(XYZ_M_T(ii,:));
end
timeM=((1:length(VecMag_T))/fs)*1000;
%% =============================================================================
% ================================== Plotting ==================================
ECG3 = figure('visible','off');
set (ECG3, 'Units', 'normalized', 'outerposition', [0,0,1,1]);
subplot(211)
plot(timeM,VecMag_T)
title('Time Alignment')
subplot(212)
plot(timeM,XYZ_M_T)
title('Median X, Y, and Z leads')
saveas(ECG3,strcat(Results_folder,file_ID{1},'_Median_beat.jpg'),'jpg');
%% =============================================================================
%% ================== Write Calculated Variables to .mat file ==================
Mat_folder = [Results_folder 'Mat Files' '/'];
if (exist(Mat_folder) == 0)
mkdir (Mat_folder);
end
% Save to a new MAT file
Label_beat='N';
save(strcat(Mat_folder,file_ID{1},'.mat'),'XYZ_O','Rpeaks','VecMag_T','XYZ_M_T','Beats_x_T','Beats_y_T','Beats_z_T','Label_beat');