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Accessing a file in a subfolder on PhysioNet using pn_dir #467
Description
I'm using wfdb 4.1.2, and when I try to run this code it fails with a 404:
import wfdb
record = wfdb.rdrecord('p1003/p10030753/s40735970/40735970', pn_dir='mimic-iv-ecg')
NetFileNotFoundError: 404 Error: Not Found for url: https://physionet.org/files/mimic-iv-ecg/1.0/40735970.heaLooks like this relates to hacky path parsing which there is an open (semi-complete) PR for (#346).
I also tried:
import wfdb
record = wfdb.rdrecord('40735970', pn_dir='mimic-iv-ecg/1.0/p1003/p10030753/s40735970')
NetFileNotFoundError: 404 Error: Not Found for url: https://physionet.org/files/mimic-iv-ecg/1.0/p1003/p10030753/s40735970/40735970.heaSo I played with the path, and this ends up working:
import wfdb
record = wfdb.rdrecord('40735970', pn_dir='mimic-iv-ecg/1.0/files/p1003/p10030753/s40735970')Seems a bit unintuitive to me that you have to put files in there, am I doing something wrong?
Activity
briangow commentedon Nov 14, 2023
I also struggle with correctly setting the path when using
rdrecordetc.Updating the documentation and using examples from the most complicated cases would help. I find that the link to a file in the PhysioNet project page is reliable but it might not be intuitive to everyone to go there to get an idea of what
pn_dirshould be.Ultimately, it'd be great if functions like
get_record_listworked cleanly with therecord_nameandpn_dirfromrdrecordetc. This isn't the case now. For a project like https://physionet.org/content/mimic4wdb/0.1.0/ with multiple levels ofRECORDfiles, theget_record_listfunction returns the path found in the top-levelRECORDfile. If you run it again, joining the result from the top-levelRECORDas part of thedb_dir, you get the result for the bottom-levelRECORDfile (in this project anyhow). If we documented this I think it'd be helpful. However, theget_record_listnever produces a clean result forrecord_nameandpn_dir(at least not for this project and similarly designed projects, i.e. MIMIC-IV-ECG , etc). In this case it returns the last folder and the record_name, so the user has to split the string to get just therecord_name. If we could updateget_record_listor introduce a new function (get_pn_dir_record_name) it would be helpful.tompollard commentedon Nov 16, 2023
Side note, but I would like to move the logic for interacting with the PhysioNet platform into: https://github.com/MIT-LCP/physionet, so that WFDB can focus on file formats and analysis tools.