spindles dection issue

[chensnbetter]

When trying to detect spindles, it always shows that no spindles were found in data.

import mne
raw = mne.io.read_raw_edf('C://Users//ASUS//Desktop//yasa_example_night_young.edf', preload=True)
raw
print(raw.ch_names)
raw.drop_channels(['ROC-A1', 'LOC-A2', 'EMG1-EMG2', 'EKG-R-EKG-L'])
chan = raw.ch_names
print(chan)
print(raw.info['sfreq'])
raw.resample(100)
sf = raw.info['sfreq']
sf
raw.filter(0.3, 45)
data = raw.get_data(units="uV")
print(data.shape)
import pandas as pd
hypno = pd.read_csv("C://Users//ASUS//Desktop//yasa_example_night_young_hypno.csv", squeeze=True)
hypno
import yasa
yasa.plot_hypnogram(hypno);
yasa.sleep_statistics(hypno, sf_hyp=1/30)
counts, probs = yasa.transition_matrix(hypno)
probs.round(3)
import numpy as np
np.diag(probs.loc[2:, 2:]).mean().round(3)
hypno_up = yasa.hypno_upsample_to_data(hypno, sf_hypno=1/30, data=raw)
print(len(hypno_up))
yasa.plot_spectrogram(data[chan.index("C4-A1")], sf, hypno_up);
yasa.bandpower(raw)
yasa.bandpower(raw, relative=False, bands=[(1, 9, "Slow"), (9, 30, "Fast")])
bandpower = yasa.bandpower(raw, hypno=hypno_up, include=(2, 3, 4))
bandpower.to_csv("bandpower.csv")
sp = yasa.spindles_detect(raw, hypno=hypno_up, include=(2, 3))

It didn't go well while doing it with data other than the sample data of yasa. So I tried it with the sample data of yasa, and the same error appears.

[remrama]

Hi @chensnbetter . I just tried replicating this issue but everything seemed to work fine for me. The first thing I did was trim the code down to the essentials needed for the spindle detection and ran this:

import mne
import pandas as pd
import yasa

raw_fname = "./yasa_example_night_young.edf"
hypno_fname = "./yasa_example_night_young_hypno.csv"
raw = mne.io.read_raw_edf(raw_fname, preload=True)
raw.drop_channels(['ROC-A1', 'LOC-A2', 'EMG1-EMG2', 'EKG-R-EKG-L'])
raw.resample(100)
raw.filter(0.3, 45)
hypno = pd.read_csv(hypno_fname, squeeze=True)
hypno_up = yasa.hypno_upsample_to_data(hypno, sf_hypno=1/30, data=raw)
sp = yasa.spindles_detect(raw, hypno=hypno_up, include=(2, 3))

That worked well for me, spindles were detected.

Then I thought maybe some of the other functions might have accidentally been modifying raw or something (mne can be sneaky with the in-place modifications). So I reran the script including all your other lines (except for the prints) and still, spindles were detected.

Could you try re-running this with the trimmed down code? Make sure you're up to date on YASA (I'm using YASA v0.6.2 in a Python v3.10.6 environment), and also be sure to exit and re-open a new iPython session if you're using something like that (to clear out any existing variables). Probably download fresh copies of the sample data to be sure as well.

[chensnbetter]

Package Version

---

antropy 0.1.4
appdirs 1.4.4
asttokens 2.1.0
backcall 0.2.0
certifi 2022.9.24
charset-normalizer 2.1.1
colorama 0.4.6
contourpy 1.0.6
cycler 0.11.0
debugpy 1.6.3
decorator 5.1.1
entrypoints 0.4
executing 1.2.0
fonttools 4.38.0
fsspec 2022.11.0
idna 3.4
ipykernel 6.17.1
ipython 8.6.0
ipywidgets 8.0.2
jedi 0.18.2
Jinja2 3.1.2
joblib 1.2.0
jupyter_client 7.4.7
jupyter_core 5.0.0
jupyterlab-widgets 3.0.3
kiwisolver 1.4.4
littleutils 0.2.2
llvmlite 0.39.1
lspopt 1.2.0
MarkupSafe 2.1.1
matplotlib 3.6.2
matplotlib-inline 0.1.6
mne 1.2.2
nest-asyncio 1.5.6
numba 0.56.4
numpy 1.23.5
outdated 0.2.2
packaging 21.3
pandas 1.5.2
parso 0.8.3
pickleshare 0.7.5
Pillow 9.3.0
pip 22.3.1
platformdirs 2.5.4
pooch 1.6.0
prompt-toolkit 3.0.33
psutil 5.9.4
pure-eval 0.2.2
Pygments 2.13.0
pyparsing 3.0.9
pyriemann 0.3
python-dateutil 2.8.2
pytz 2022.6
pywin32 305
PyYAML 6.0
pyzmq 24.0.1
requests 2.28.1
scikit-learn 1.1.3
scipy 1.9.3
seaborn 0.12.1
setuptools 63.2.0
six 1.16.0
sleepecg 0.5.2
stack-data 0.6.1
stochastic 0.7.0
tensorpac 0.6.5
threadpoolctl 3.1.0
tornado 6.2
tqdm 4.64.1
traitlets 5.5.0
urllib3 1.26.13
wcwidth 0.2.5
widgetsnbextension 4.0.3
yasa 0.6.2

I have reinstalled python and other related installation packages. And that is also useless.

[raphaelvallat]

Thanks for this. Can you please share here your Jupyter notebook? Please make sure to add a cell at the end with:

print(raw)
print(hypno)
sp.summary()

[chensnbetter]

[raphaelvallat]

I really have no idea what's going on unfortunately 😕 Can you try running the other YASA example notebooks here? https://github.com/raphaelvallat/yasa/tree/master/notebooks

[chensnbetter]

Thanks, I will try the other notebooks.
Meanwhile, I would like to ask, is there any problem in the following process?

[chensnbetter]

Strangely, why can I detect slow waves successfully?

[raphaelvallat]

Hmmm, there must be something specific about the steps/sub-functions in the spindles_detect function

[raphaelvallat]

Opened an issue here: #107 Let's move the conversation there