Bug when read raw cnt file

[ZiyiTsang]

Description of the problem

Hi who it may concern, I am writing the code to read cnt when it occur the error as follow:

Error
File /mnt/nvme2n1/(xxxxxxxxxx)/lib/python3.10/site-packages/mne/io/cnt/cnt.py:340, in _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format, header)
338 # See: PR #12393
339 annotations = _read_annotations_cnt(input_fname, data_format="int16")
--> 340 if annotations.onset[-1] * sfreq > n_samples:
341 n_bytes = 4
342 n_samples = n_samples_header

IndexError: index -1 is out of bounds for axis 0 with size 0

Steps to reproduce

data = mne.io.read_raw_cnt('1_1.cnt', preload=True)

(then orrur happen...)

Link to data

This is a file in SEED-GER dataset. I can send you the file email for debug purpose only.

Expected results

Expected run perfectly

Actual results

Traceback

IndexError Traceback (most recent call last)
Cell In[15], line 3
1 with warnings.catch_warnings():
2 warnings.simplefilter("ignore")
----> 3 data = mne.io.read_raw_cnt('/mnt/xxxxxxxxxxx/SEED_GER/German/01-EEG-raw/1_1.cnt', preload=True)

File /mnt/xxxxxxxxxxx/python3.10/site-packages/mne/io/cnt/cnt.py:248, in read_raw_cnt(input_fname, eog, misc, ecg, emg, data_format, date_format, header, preload, verbose)
163 @fill_doc
164 def read_raw_cnt(
165 input_fname,
(...)
175 verbose=None,
176 ) -> "RawCNT":
177 """Read CNT data as raw object.
178
179 .. Note::
(...)
246 .. versionadded:: 0.12
247 """
--> 248 return RawCNT(
249 input_fname,
250 eog=eog,
251 misc=misc,
252 ecg=ecg,
253 emg=emg,
254 data_format=data_format,
255 date_format=date_format,
256 header=header,
257 preload=preload,
258 verbose=verbose,
259 )

File /mnt/xxxxxxxxxxxx/python3.10/site-packages/mne/io/cnt/cnt.py:531, in RawCNT.init(self, input_fname, eog, misc, ecg, emg, data_format, date_format, header, preload, verbose)
528 _date_format = "%m/%d/%y %H:%M:%S"
530 input_fname = path.abspath(input_fname)
--> 531 info, cnt_info = _get_cnt_info(
532 input_fname, eog, ecg, emg, misc, data_format, _date_format, header
533 )
534 last_samps = [cnt_info["n_samples"] - 1]
535 super().init(
536 info,
537 preload,
(...)
542 verbose=verbose,
543 )

File /mnt/xxxxxxxxxxxxxxxx/python3.10/site-packages/mne/io/cnt/cnt.py:340, in _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format, header)
338 # See: PR #12393
339 annotations = _read_annotations_cnt(input_fname, data_format="int16")
--> 340 if annotations.onset[-1] * sfreq > n_samples:
341 n_bytes = 4
342 n_samples = n_samples_header

IndexError: index -1 is out of bounds for axis 0 with size 0

Additional information

Platform Linux-5.15.0-124-generic-x86_64-with-glibc2.31
Python 3.10.15 (main, Oct 3 2024, 07:27:34) [GCC 11.2.0]
Executable /mnt/nvme2n1/zengziyi/anaconda/envs/LGU/bin/python
CPU x86_64 (112 cores)
Memory 1007.5 GB

Core
├☑ mne 1.8.0 (latest release)
├☑ numpy 1.26.4 (MKL 2023.1-Product with 56 threads)
├☑ scipy 1.13.1
└☑ matplotlib 3.9.2 (backend=module://matplotlib_inline.backend_inline)

Numerical (optional)
├☑ sklearn 1.5.2
├☑ pandas 2.2.2
├☑ h5io 0.2.4
└☐ unavailable numba, nibabel, nilearn, dipy, openmeeg, cupy, h5py

Visualization (optional)
├☑ ipywidgets 8.1.5
└☐ unavailable pyvista, pyvistaqt, vtk, qtpy, ipympl, pyqtgraph, mne-qt-browser, trame_client, trame_server, trame_vtk, trame_vuetify

Ecosystem (optional)
├☑ mne-icalabel 0.7.0
└☐ unavailable mne-bids, mne-nirs, mne-features, mne-connectivity, mne-bids-pipeline, neo, eeglabio, edfio, mffpy, pybv

[welcome]

Hello! 👋 Thanks for opening your first issue here! ❤️ We will try to get back to you soon. 🚴

[larsoner]

Indeed this looks like it's probably a bug where we assume that there is at least one annotation, but there are none.

If you change

mne-python/mne/io/cnt/cnt.py

Line 340 in f5d043a

if annotations.onset[-1] * sfreq > n_samples:

To

if len(annotations) and annotations.onset[-1] * sfreq > n_samples:

does it work? If so, PR welcome for this quick fix!

[ZiyiTsang]

Ok, trying to work on it!

[ZiyiTsang]

Yes, it work for me. I have create PR #12986 to quick fix this.
This is my first time creating PR. If anything wrong, kindly inform me. Thanks.

[ZiyiTsang]

As PR complete, I close this issue. Thanks!