One malformed signal in mimic3 matched?
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Description
Hi,
I've been using wfdb-python to parse numerics from the mimic3 waveforms database at large. I've found just one file that appears to be unreadable by wfdb, from patient p086831. Here's a minimum example (pulling from the online database):
import wfdb
rec_id = "p086831-2130-12-29-18-28n"
# rec_path = "mimic3wdb/1.0/matched/p08/p086831/"
rec_path = "mimic3wdb-matched/1.0/p08/p086831/"
rec = wfdb.rdrecord(rec_id, pn_dir=rec_path)
ValueError Traceback (most recent call last)
Cell In[6], line 6
4 # rec_path = "mimic3wdb/1.0/matched/p08/p086831/"
5 rec_path = "mimic3wdb-matched/1.0/p08/p086831/"
----> 6 rec = wfdb.rdrecord(rec_id, pn_dir=rec_path)
...
File .../venv/lib/python3.11/site-packages/wfdb/io/_signal.py:2051, in _check_sig_dims(sig, read_len, n_sig, samps_per_frame)
2049 for ch in range(n_sig):
2050 if len(sig[ch]) != samps_per_frame[ch] * read_len:
-> 2051 raise ValueError("Samples were not loaded correctly")
ValueError: Samples were not loaded correctly
This also occurs when pulling the respective .hea and .dat files locally and using wfdb from there.
Perhaps this is an issue with the MIMIC file itself, but I wanted to start here, since I'm not sure how to tell. Might this be a MIMIC bug, or is this a wfdb issue?
Thanks in advance--
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Research direction
Start by reproducing the example with wfdb.rdrecord for p086831-2130-12-29-18-28n, both from the online database and from the local .hea and .dat files. Inspect wfdb/io/_signal.py around _check_sig_dims and compare the declared sample dimensions with the loaded data. Done means determining whether the mismatch originates in wfdb or the MIMIC file and recording the evidence.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100