Analyze MIMIC III waveform data directly in Matlab

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Ram Krishnan
Ram Krishnan 2024-7-10
回答： Ram Krishnan 2024-10-6
I would like to analyze MIMIC III waveform data (mainly PPG and ABP) directly in Matlab on a MacOS without going through Google or AWS database queries. Has anyone done this? Can you advise me on the best way?
Thanks
Ram

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回答（2 个）

William Rose
William Rose 2024-7-10
@Ram Krishnan,
After you reigtser on the physionet site, you may use the package here
https://archive.physionet.org/physiotools/matlab/wfdb-app-matlab/
You should also check out the use of "wget" to download files from the MIMIC-III database, as described here:
https://physionet.org/content/mimic3wdb/1.0/30/3000003/#files-panel
(Scroll down to wget, or search the page for wget.)
wget is not part of Mac OS, but you can get it. Google "wget for Mac". I am not a Mac person.
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Ram Krishnan
Ram Krishnan 2024-7-11
William,
That is hugely helpful as all the exploring I did on Matlab's Help site and on Google were unproductive. I'll try both tools out.
Thanks
Ram

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Ram Krishnan
Ram Krishnan 2024-10-6
clc;clear;close all;
fileDir = '/myMimicDir/';
recList = append(fileDir,'mimic3wdbRecordsWithPpgANDbp.txt');
fileID = fopen(recList);
numRecs = 10; % number of data records to read and write into excel
numSamples = 1000000; % number of samples to read and write in each record
for i = 1:numRecs
wdbRec(i) = textscan(fileID,'%s \n');
% wdbRec{i}
end
fclose(fileID);
for i = 1:numRecs
[fileNameTemp,~,~] = wfdbdesc(char(wdbRec{i}));
fileName = struct2cell(fileNameTemp);
[~,~,numVar] = size(fileName);
for j=1:numVar
varName = fileName(9,1,j);
if contains(varName,'PLETH')
ppgCol = j;
elseif contains(varName,'ABP')
abpCol = j;
end
end
recName = cell2mat(wdbRec{1,i});
fprintf('Record number %d \n',i);
fprintf('Now in rdsamp.. \n')
[signal,Fs,tm]=rdsamp(recName,[ppgCol abpCol],numSamples);
writeFileDir = '/myMimicDir/PPG-ABP dataset created by ReadMimic3wdbFileList_092324/';
recLabel = recName(end-23:end); % use last 23 char of recName to create a spreadsheet name
writeFileName = append(writeFileDir,recLabel);
excelFileName = append(writeFileName,'.xlsx');
fprintf('Now in writematrix..\n')
writematrix(signal,excelFileName);
%%% plot for visualizing signals
% figure
% plot(tm(5000:10000),signal(5000:10000,1)); % first 5000 samples may be noise
% figure
% plot(tm(5000:10000),signal(5000:10000,2))
end

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