what changes would you recommend

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Manav Divekar
Manav Divekar on 29 Nov 2021
I am trying to do muscle fatigue analysis this is how far i have made. What changes i should make so that my code works.
for the acquired data set.
% 2 sec Time Trials
clear
clc
close all
files = dir('*.txt'); % Returns all the files and folders in the directory
fileTable = struct2table(files);
numOfFiles = height(fileTable);
for k = 1:numOfFiles % check for time trial files and excludes MVIC
if strfind(fileTable.name{k}, 'sec')
secfiles{k} = fileTable.name{k};
end
end
allsecfiles = secfiles(:,~cellfun(@isempty,secfiles(1,:)));
masterData = struct;
for j = 1:length(allsecfiles) % compile file name information
file_info(:,j) = split(allsecfiles(j), "_");
masterData(j).group = file_info(1,j);
masterData(j).time = file_info(2,j);
masterData(j).trial = extractBefore(file_info(4,j),'.');
end
timetrials = {'2sec';'5sec';'10sec'}; % define iterations/categories of files
newfig = 1; % beginning figure
r=1;
for t = 1:length(timetrials) % iterate for each time duration
timetrialfiles = find(strcmp(file_info(2,:),timetrials{t})); % index files that correspond to selected time duraiton
gettimefiles = allsecfiles(timetrialfiles); % files that correspond to time duration
for s = 1:length(gettimefiles) % iterate for each trial (2 or 3)
for c = 1:2 % iterate for columns for bicep and tricep
if c==1
musc_c = 'Bicep'; % Bicep data located in first 8 columns
timecol = 1;
emgcol = 2;
else
musc_c = 'Tricep'; % Tricep data located in second 8 columns
timecol = 9;
emgcol = 10;
end
imptimetrials = readtable(char(gettimefiles(s)));
time = table2array(imptimetrials(:,timecol));
emg = table2array(imptimetrials(:,emgcol));
figure(newfig)
plot(time,emg,'b') % plot raw EMG data in blue
hold on
% determine where to split concentric and eccentric data based on file name
idc = strfind(timetrials,'2sec');
idx = ~cellfun('isempty',idc);
findidx = find(idx==1);
if findidx == t
cut = 1;
endtime = 2;
else
idc = strfind(timetrials,'5sec');
idx = ~cellfun('isempty',idc);
findidx = find(idx==1);
if findidx == t
cut = 2.5;
endtime = 5;
else
cut = 5;
endtime = 10;
end
end
con = find(time < cut & time > 0); % first half of time trial
ecc = find(time > cut & time < endtime);
contime = time(con);
conemg = emg(con);
ecctime = time(ecc);
eccemg = emg(ecc);
figure(newfig)
plot(contime,conemg, 'Color','#D95319')
hold on
plot(ecctime,eccemg, 'Color','#EDB120') % plot second half in yellow
xlabel('Time (s)')
ylabel('EMG Response (mV)')
legend(sprintf('%s EMG',musc_c), 'Concentric', 'Eccentric')
title(sprintf('%s: %s EMG vs Time [Trial %d]',timetrials{t},musc_c,s))
hold off
newfig = newfig+1;
figure(newfig)
% Plot Concentric Rectified
subplot(1,2,1)
plot(contime,conemg,'b')
hold on
smooth_con = smooth(abs(conemg - mean(conemg)));
plot(contime,smooth_con,'k')
hold on
RMScon = sqrt(movmean(smooth_con.^2,500));
plot(contime,RMScon,'r')
legend('RawEMG','Rectified EMG','Moving Average')
title(sprintf('%s %s EMG: Concentric Contraction vs Time',timetrials{t}, musc_c))
xlabel('Time (s)')
ylabel('EMG Response (mV)')
hold off
% Plot Eccentric Rectified
subplot(1,2,2)
plot(ecctime, eccemg, 'b')
hold on
smooth_ecc = smooth(abs(eccemg-mean(eccemg)));
plot(ecctime, smooth_ecc,'k')
hold on
RMSecc = sqrt(movmean(smooth_ecc.^2,500));
plot(ecctime,RMSecc,'r')
legend('RawEMG','Rectified EMG','Moving Average')
title(sprintf('%s %s EMG: Eccentric Contraction vs Time',timetrials{t}, musc_c))
xlabel('Time (s)')
ylabel('EMG Response (mV)')
hold off
newfig = newfig+1;
%% Rectified and Integrated EMG
% Concentric
figure(newfig)
subplot(1,2,1)
plot(contime,smooth_con,'k')
hold on
intCon = cumtrapz(RMScon);
yyaxis right
plot(contime,intCon,'g')
legend('Rectified EMG','Integrated EMG')
title(sprintf('%s %s EMG: Concentric Contraction vs Time',timetrials{t},musc_c))
xlabel('Time (s)')
ylabel('EMG Response (mV-s)')
yyaxis left
ylabel('EMG Response (mV)')
hold off
% Eccentric
subplot(1,2,2)
plot(ecctime,smooth_ecc,'k')
hold on
intEcc = cumtrapz(RMSecc);
yyaxis right
plot(ecctime, intEcc,'g')
legend('Rectified EMG','Integrated EMG')
title(sprintf('%s %s EMG: Eccentric Contraction vs Time',timetrials{t},musc_c))
xlabel('Time (s)')
ylabel('EMG Response (mV-s)')
yyaxis left
ylabel('EMG Response (mV)')
hold off
newfig = newfig+1;
maxRMScon(r,c) = max(RMScon);
maxRMSecc(r,c) = max(RMSecc);
maxINTcon(r,c) = max(intCon);
maxINTecc(r,c) = max(intEcc);
fourier_con = smooth_con.*1000;
fourier_ecc = smooth_ecc.*1000;
fs = 2000;
tau = 1/fs;
lenCon = length(fourier_con);
lenEcc = length(fourier_ecc);
fftCon = abs(fft(fourier_con));
fftEcc = abs(fft(fourier_ecc));
truncCon = fftCon(1:lenCon/2+1);
truncEcc = fftEcc(1:lenEcc/2+1);
truncCon(2:end-1) = truncCon(2:end-1).*2;
truncEcc(2:end-1) = truncEcc(2:end-1).*2;
fc = ((0:(lenCon/2))./lenCon).*fs;
fe = ((0:(lenEcc/2))./lenEcc).*fs;
freqrange = 20:10:500;
for fr = 1:length(freqrange)-1
freqcon = [];
freqecc = [];
freqcon(fr) = medfreq(truncCon(freqrange(fr):freqrange(fr+1)),fs);
freqecc(fr) = medfreq(truncEcc(freqrange(fr):freqrange(fr+1)),fs);
end
[pMaxCon,pMaxConLocs] = max(freqcon);
[pMaxEcc,pMaxEccLocs] = max(freqecc);
figure(newfig)
subplot(1,2,1)
xline(pMaxCon, '--r','LineWidth',2);
hold on
plot(fc,truncCon,'b-o')
hold on
xlim([20 500])
xlabel('Frequency (Hz)')
ylabel('Power Spectrum')
title(sprintf('%s %s EMG: Concentric Power Spectrum',timetrials{t},musc_c))
legend(sprintf('Median f = %d Hz', pMaxCon),sprintf('Power: %s Concentric %s', musc_c, timetrials{t}))
hold off
subplot(1,2,2)
xline(pMaxEcc, '--r','LineWidth',2);
hold on
plot(fe,truncEcc,'b-o')
hold on
xlim([20 500])
xlabel('Frequency (Hz)')
ylabel('Power Spectrum')
title(sprintf('%s %s EMG: Eccentric Power Spectrum',timetrials{t},musc_c))
legend(sprintf('Median f = %d Hz', pMaxEcc),sprintf('Power: %s Eccentric %s', musc_c, timetrials{t}))
hold off
newfig = newfig+1;
for myfig = 1:newfig-1
saveas(myfig,sprintf('%s_Fig%d.png', musc_c, myfig))
end
end
r = r+1;
end
end

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