One malformed signal in mimic3 matched?

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Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
python
Domain
data

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.

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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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