Access database in Physionet's ptbdb by Matlab

Question

I set up the system first by

[old_path]=which(\'rdsamp\');if(~isempty(old_path)) rmpath(old_path(1:end-8)); end
wfdb_url=\'http://physionet.org/physiotools/m         


        

Answer 1

If you run physionetdb("ptdb",1) it will download the files to your computer. You will then be able to see the available records in the <current-dir>/ptdb/

Source: physionetdb function documentation. You are interested in the DoBatchDownload parameter.

After downloading it, I believe every command from the toolbox will check if you have the files locally before fetching from the server (as long as you give the function the correct path to the local files).

Answer 2

The problem is that the data unit "100" does not exist in the database ptbdb.

I run finally successfully after waiting 35 minutes with 100Mb cable broadband:

db_list = physionetdb('ptbdb')

and get not complete data finally to the patient 54 - there should be 294 patients.

'ptbdb/patient001/s0014lre' 'ptbdb/patient001/s0014lre' ... cut ...

The main developer, Ikaro's' answer helped me to wait so long:

The WFDB Toolbox connects to PhysioNet's file server. The databases
accessible through the WFDB Toolbox are not SQL database, they consist
of flat files. The error message that you are getting regarding the
ptdb/100 database is because you are attempting to get a record that
does not exist on the database.

For more information on a particular database or record in PhysioNet please type:

help physionetdb

and

physionetdb('ptdb')

This flat file system is really a bottle neck in the system. It would be a good time to change to SQL.