How to read a .dat file containing an ECG signal?

Question

Susan 2022-8-5

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1774890-how-to-read-a-dat-file-containing-an-ecg-signal

评论： Achamma Thomas 2022-8-13

SE8ECG4E.zip

Hi,

I have an ECG signal contains data collected from 12 leads, saved in a .dat file (attached here). Could someone please help me to read this file? I've already installed WFDB toolbox to read the file, however, it's not able to search locally for the file and so not able to read it. I've tried to read data using rdann.m file however it needs an annotator file that I don't have. Any help would be greatly appreciated!

Thanks,

Susan

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Answer 1

Star Strider 2022-8-6

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1774890-how-to-read-a-dat-file-containing-an-ecg-signal#answer_1021970

PhysioBank used to be much friendlier than it now is.

I have no idea what records you’re interested in, however the easiest way to work with it is to go to the PhysioBank ATM then select the database you’re interested in and then use the Toolbox drop-down menu and select one of the ‘Export as ...’ options to get the data in a relatively easy-to-import file. (I suggest the .CSV option if you want to post it here as an attachment, since the online Run feature here still doesn’t work and play well with .mat files, and .CSV files are easy to work with.)

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Star Strider 2022-8-6

在 MATLAB Online 中打开

‘... however, it's not able to search locally for the file ...’

It may be necessary to tell it where the file is by providing the full path name. The fileparts and fullfile functions may be necessary to do this. The other option is to use the movefile function to copy the .dat file to the same directory as the function that reads it (or wherever that function would look for it). I generally use the files I can easily get through the ATM, so I don’t need the other PhysioNet files, and so have no experience with them.

My note in that post is the best I can do. If possible, download the appropriate .zip file from PhysioNet since it will contain all the other appropriate files. There is a ‘00735.atr’ annotation file in the link I provided earlier (and re-reference here) that may be what you need for the PhysioNet function to work. I suggest downloading all the 00735.* files and put them in the same directory so you have them in the event that you need them.

Otherwise, it appears to be a binary file, and while it’s certainly possible to read binary files with the fread function, my attempts at guessing the necessary parameters in order to read it have not been successful.

Uz = unzip('https://www.mathworks.com/matlabcentral/answers/uploaded_files/1089450/SE8ECG4E.zip')
Uz = 1×1 cell array
    {'SE8ECG4E.DAT'}
datfile = readcell(Uz{1})
datfile = 12417×24 cell array
    {'          B41741881V1.20   None    1024  CCCCCCCCFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFI  II V1 V2 V3 V4 V5 V6                                                                   10     110  20.05OFF 60                                     22222222ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ22'                                                                                                                   }    {[                                                                                                                                                                                                                                                                                7]}    {'2804:25                                                                                                                                                                                                              ?1A!ø $¿:Å¨S!"¶'}    {1×1 missing                                  }    {1×1 missing                                              }    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}    {1×1 missing}
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.

Susan 2022-8-6

在 MATLAB Online 中打开

rdann.m

Thanks again for your quick response! Truly appreciate it.

As you mentioned, I tell it where the file is by providing the full path name.

>> file = "C:\User\Desktop\test\database\mitdb\SE8ECG4E.dat";
[filepath,name,ext] = fileparts(file)
filepath = 
    "C:\User\Desktop\test\database\mitdb"
name = 
    "SE8ECG4E"
ext = 
    ".dat"
    
    or:
     filepath = fullfile('C:\Users\Desktop\test\database','mitdb','SE8ECG4E.dat')

But here is the error that I get

     [signal, fs, tm] = rdsamp(filepath);
Error using rdsamp (line 204)
Could not find record: C:\User\Desktop\test\database\mitdb\SE8ECG4E. Search path is set to: '.
C:\User\Desktop\test\mcode\..\database\http://physionet.org/physiobank/database/'

then I copied the SE8ECG4E.dat file and paste it to "C:\User\Desktop\test\mcode" , and I got the same error as before

[signal, fs, tm] = rdsamp('C:\User\Desktop\test\mcode\SE8ECG4E.DAT');
Error using rdsamp (line 204)
Could not find record: C:\User\Desktop\test\mcode\SE8ECG4E.DAT. Search path is set to: '.
C:\User\Desktop\test\mcode\..\database\http://physionet.org/physiobank/database/'

First question: I wasn't able to take advantage of the movefile function as you suggested. Could you please kindly tell me what I am doing wrongly?

SourceFile = 'C:\User\Desktop\test\SE8ECG4E.DAT';
destinationFolder = 'C:\User\Desktop\test\database\mitdb'
>> movefile SourceFile destinationFolder
Error using movefile
Cannot copy or move a file or directory onto itself.

Here is how my folder and files in it looks like.

Then I chain the WFDB_path in the wfdbloadlib.m line 50 from [] to the following address to make sure the package searchs locally instead of searching online.

%WFDB_PATH: If empty, will use the default given config.WFDB_PATH
%this is where the toolbox searches  for data files (*.dat, *.hea etc).
%When unistalling the toolbox, you may wish to clear this directory to save space.
%See http://www.physionet.org/physiotools/wag/setwfd-1.htm for more details.
WFDB_PATH='C:\User\Desktop\test\database\';%[];

However, still I get the same error as above.

Anyway, THANK YOU SO MUCH for your help and suggestions! I haven't thought about this possibility that you suggested, i.e., "download the appropriate .zip file from PhysioNet since it will contain all the other appropriate files. There is a ‘00735.atr’ annotation file in the link I provided earlier (and re-reference here) that may be what you need for the PhysioNet function to work."

I downloaded the files and working on it! the rdann.m file is attached here too. No success so far and getting an error "Index exceeds Java array dimensions", but I'm on it and it worths a try!

Star Strider 2022-8-10

在 MATLAB Online 中打开

Well, I still can’t read the binary file (the first one). The second file is nothing I’ve ever seen before. I have no idea what its sampling frequency is, however it just looks like some sort of noise. It doesn’t make any sense even after lowpass filtering (guessing at the cutoff frequency). It’s certainly not a normal EKG, and the amplitude is too high for any physiological signal I’ve ever encountered, so there must be some sort of scaling factor involved.

LD1 = load(websave('hdr','https://www.mathworks.com/matlabcentral/answers/uploaded_files/1093815/hdr.mat'))

LD1 = struct with fields:

hdr: {' B41741881V1.20 None 1024 CCCCCCCCFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFI II V1 V2 V3 V4 V5 V6 10 110 20.05OFF 60 22222222ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ22/08/1004:11 Ô0Aô (&¿/ˆµ²D7!Ž"'}

LD2 = load(websave('MeasInfo','https://www.mathworks.com/matlabcentral/answers/uploaded_files/1093845/MeasInfo.mat'))

LD2 = struct with fields:

MeasInfo: [387651×1 double]

MeasInfo = LD2.MeasInfo;

x = 0:numel(MeasInfo)-1;

figure

plot(x, MeasInfo)

grid

figure

plot(x, MeasInfo)

grid

xlim([0 1000])

MeasInfoFilt = lowpass(MeasInfo, 0.05, 1, 'ImpulseResponse','iir');

figure

plot(x, MeasInfoFilt)

grid

xlim([0 1000])

I am at a complete loss here.

.

Susan 2022-8-11

编辑：Susan 2022-8-11

在 MATLAB Online 中打开

Data.zip

@Star Strider Thanks again for your detailed response. Even though I haven't solved the problem yet, your answers always are beneficial to me and help me to have a better understanding of the possible solutions to this problem. I truly appreciate your time and help!

I collected another set of data. It's attached here (Data.zip that contains .dat file). Then I used the following code

%Open data file
Fid = fopen('\SE8ECG4E.DAT');
MeasData = fread(Fid,'int');
fclose(Fid);
Fs = 1024; % sample rate
%Plot data
figure;plot((0:length(MeasData)-1)*(1/(Fs*4)),MeasData)

This is what I get

When I zoom in I get

As you mentioned, "the amplitude is too high for any physiological signal".

I dug more into the collected data and this is what I found:

there is a recording gain of 2mV = 20mm/mV
Sample rate is 1024
Some parameters are given for filtering: HP filter= 0.05 and LP Filter = 60
Recording time: 00:02:07

I expect the signal length to be Sample rate* Recording time = 1024*127 = 130048 but the size of data is 520536 which is almost 4 times greater than 130048. Any idea why this is the case?

Could you please let me know if knowing any of this information can help us to plot a clean ECG signal?

Star Strider 2022-8-11

在 MATLAB Online 中打开

Susan_MeasData.zip

Try this —

Uz = unzip('Susan_MeasData.zip')

Uz = 1×1 cell array

{'Susan_MeasData.txt'}

MeasData = readmatrix(Uz{1});

MeasData = MeasData/max(MeasData(end-5000:end)); % Normalise Amplitude

Fs = 1024; % sample rate

Fn = Fs/2;

L = numel(MeasData);

t = linspace(0, L-1, L)/Fs; % Time Vector

DataMask = 13000:L;

MeasDataFilt = sgolayfilt(MeasData, 3, 101); % Filter EKG

%Plot data

figure

subplot(2,1,1)

plot(t,MeasData)

grid

xlim([min(t) max(t)])

subplot(2,1,2)

plot(t,MeasDataFilt)

grid

xlim([min(t) max(t)])

figure

subplot(2,1,1)

plot(t,MeasData)

grid

xlim([13 20])

subplot(2,1,2)

plot(t,MeasDataFilt)

grid

xlim([13 20])

I could not get the frequency-selective filters to produce the result I want, so I went with sgolayfilt with satisfactory results for the entire record. (It looks normal to me, although I do not trust the sampling frequency because the intervals do not appear to be correct, although the relative intervals as fractions of the R-R intervals are.)

The file contains the extracted data as a text file.

.

Susan 2022-8-12

@Achamma Thomas Hey! I haven't been able to solve that issue yet. But it seems your data has the same structure of mine. There is a header, raw data, and maybe sth at the end. Happy to brianstorm and find a solution!

Achamma Thomas 2022-8-13

@Susan yes will surely share if I find a solution, meanwhile do let me know if you find one too.

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How to read a .dat file containing an ECG signal?

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How to read a .dat file containing an ECG signal?

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