Accessing a file in a subfolder on PhysioNet using pn_dir
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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.hea
Looks 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.hea
So 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?
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- Read the whole issue, then the project's contributing guide.
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Research direction
Start at wfdb.rdrecord and follow how record and pn_dir are combined for PhysioNet downloads. Reproduce both failing examples, then read the semi-complete PR #346 for the existing path-parsing approach. Done means nested MIMIC-IV-ECG records resolve without requiring an unintuitive files segment, with regression coverage for the shown paths.
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Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100