Difficulties with WFDB toolkit in Matlab

I downloaded the WFDB Toolbox for Matlab onto my Mac and successfully ran the demonstration tests to prove that the download had happened.

However, when I try to open and examine the MIMIC2 database, I am running into what seems to be path problems. I used rdsamp to open the database (from the command window) as follows and get the error message right below:

>> [signal,Fs,tm]=rdsamp('mimic2wdb/30', [1 3 5],1000);

Error using rdsamp (line 203)

Could not find record: mimic2wdb/30. Search path is set to: '. /Users/ramkrishnan/Desktop/MIMIC to Matlab/mcode/../database/

http://physionet.org/physiobank/database/'

I also tried

urlread(['http://physionet.org/physiobank/database/' 'mimic2wdb/30' '/RECORDS'],1)

but got an error that the records were too long.

By the way, the demo with the MITDB record appears to work because it (MITDB) seems to be loaded onto my drive. The problem is accessing the remote physionet db.

Anybody have suggestions on how to open and examine the MIMIC2 or MIMIC3 db from Matlab?

Thanks

Ram

[Ram Krishnan]

I finally did get rdsamp to work and was able to download the appropriate records. The key was to address the record number specifically as follows:

[sig, Fs, tm] = rdsamp('mimic3wdb/31/3141595/',[],1000);

Similarly, when I tried to download matched records, I had to be even more specific, as follows:

[sig, Fs, tm] = rdsamp('mimic3wdb/matched/p00/p001457/p001457-2194-10-15-19-02',[],100);

regards

Ram

Answer 1

[Nidhi Sawant]

I was facing issues reading .dat files (WFDB format) in MATLAB due to errors with the WFDB toolbox, especially while trying to load signal and annotation data from PhysioNet datasets. Since the MATLAB WFDB integration wasn't working reliably (e.g., missing JAR files, unresolved classes), I created a workaround using Python inside MATLAB.

I used the Python wfdb package and called it from MATLAB using pyrunfile. This approach reads the .dat files and returns the signals and annotations correctly into MATLAB.

I’ve shared a complete working example here:

🔗 GitHub Repository – Read WFDB .dat Files in MATLAB Using Python

This may help others dealing with similar toolbox compatibility issues.

Let me know if you have suggestions or need help setting it up!