Description of the problem
I get a Type Error when I use annotate_muscle_zscore() method. I think its a bug.
Steps to reproduce
import numpy as np
import mne
from copy import deepcopy as dpcpy
from mne.preprocessing import annotate_muscle_zscore
np.random.seed(10)
data = np.random.rand(24,1024)
data1 = np.random.rand(24,251)
data_ = np.concatenate((data, data1),axis=1)
ch_names = ["Fp1", "Fp2", "F3", "F4", "C3", "C4", "P3", "P4", "O1", "O2", "F7", "F8", "T7", "T8", "P7", "P8", "Fz", "Cz", "Pz", "M1", "M2", "AFz", "CPz", "POz"]
montage = mne.channels.make_standard_montage('standard_1020')
info = mne.create_info(ch_names=ch_names, sfreq=1000, ch_types='eeg').set_montage(montage, match_case=False)
raw = mne.io.RawArray(data_,info, copy='data', verbose=False)
raw.set_eeg_reference(projection=True)
raw.notch_filter([60, 120])
threshold_muscle = 5
annot_muscle, scores_muscle = annotate_muscle_zscore(
raw,
ch_type="eeg",
threshold=threshold_muscle,
min_length_good=0.2,
filter_freq=[110, 140],
)
Link to data
No response
Expected results
To get the annotations for segments that likely contain muscle artifacts.
Actual results
TypeError Traceback (most recent call last)
Cell In[31], line 3
1 threshold_muscle = 5
----> 3 annot_muscle, scores_muscle = annotate_muscle_zscore(raw)
File :12, in annotate_muscle_zscore(raw, threshold, ch_type, min_length_good, filter_freq, n_jobs, verbose)
File c:\Users\Starboy\AppData\Local\Programs\Python\Python312\Lib\site-packages\mne\preprocessing\artifact_detection.py:106, in annotate_muscle_zscore(raw, threshold, ch_type, min_length_good, filter_freq, n_jobs, verbose)
104 else:
105 ch_type = {"meg": False, ch_type: True}
--> 106 raw_copy.pick(**ch_type)
108 raw_copy.filter(
109 filter_freq[0],
110 filter_freq[1],
(...)
113 n_jobs=n_jobs,
114 )
115 raw_copy.apply_hilbert(envelope=True, n_jobs=n_jobs)
TypeError: pick() got an unexpected keyword argument 'meg'
Additional information
Platform Windows-10-10.0.22631-SP0
Python 3.9.18 (main, Sep 11 2023, 14:09:26) [MSC v.1916 64 bit (AMD64)]
Executable C:\Users\Starboy.envBMindMNE\python.exe
CPU AMD64 Family 25 Model 68 Stepping 1, AuthenticAMD (16 cores)
Memory 15.2 GB
Core
├☒ mne 1.6.0 (outdated, release 1.6.1 is available!)
├☑ numpy 1.22.4 (MKL 2023.2-Product with 8 threads)
├☑ scipy 1.11.1
├☑ matplotlib 3.5.3 (backend=QtAgg)
├☑ pooch 1.7.0
└☑ jinja2 3.1.2
Numerical (optional)
├☑ sklearn 1.3.0
├☑ numba 0.57.1
├☑ nibabel 5.1.0
├☑ nilearn 0.10.1
├☑ dipy 1.7.0
├☑ openmeeg 2.5.6
├☑ pandas 2.1.0
└☐ unavailable cupy
Visualization (optional)
├☑ pyvista 0.42.1 (OpenGL 4.6.0 Compatibility Profile Context 24.1.1.240110 via AMD Radeon(TM) Graphics)
├☑ pyvistaqt 0.0.0
├☑ vtk 9.2.6
├☑ qtpy 2.4.0 (PyQt5=5.15.4)
├☑ ipympl 0.9.3
├☑ pyqtgraph 0.13.3
├☑ mne-qt-browser 0.5.2
├☑ ipywidgets 7.7.2
├☑ trame_client 2.15.0
├☑ trame_server 2.15.0
├☑ trame_vtk 2.7.1
└☑ trame_vuetify 2.4.2
Description of the problem
I get a Type Error when I use annotate_muscle_zscore() method. I think its a bug.
Steps to reproduce
Link to data
No response
Expected results
To get the annotations for segments that likely contain muscle artifacts.
Actual results
TypeError Traceback (most recent call last)
Cell In[31], line 3
1 threshold_muscle = 5
----> 3 annot_muscle, scores_muscle = annotate_muscle_zscore(raw)
File :12, in annotate_muscle_zscore(raw, threshold, ch_type, min_length_good, filter_freq, n_jobs, verbose)
File c:\Users\Starboy\AppData\Local\Programs\Python\Python312\Lib\site-packages\mne\preprocessing\artifact_detection.py:106, in annotate_muscle_zscore(raw, threshold, ch_type, min_length_good, filter_freq, n_jobs, verbose)
104 else:
105 ch_type = {"meg": False, ch_type: True}
--> 106 raw_copy.pick(**ch_type)
108 raw_copy.filter(
109 filter_freq[0],
110 filter_freq[1],
(...)
113 n_jobs=n_jobs,
114 )
115 raw_copy.apply_hilbert(envelope=True, n_jobs=n_jobs)
TypeError: pick() got an unexpected keyword argument 'meg'
Additional information
Platform Windows-10-10.0.22631-SP0
Python 3.9.18 (main, Sep 11 2023, 14:09:26) [MSC v.1916 64 bit (AMD64)]
Executable C:\Users\Starboy.envBMindMNE\python.exe
CPU AMD64 Family 25 Model 68 Stepping 1, AuthenticAMD (16 cores)
Memory 15.2 GB
Core
├☒ mne 1.6.0 (outdated, release 1.6.1 is available!)
├☑ numpy 1.22.4 (MKL 2023.2-Product with 8 threads)
├☑ scipy 1.11.1
├☑ matplotlib 3.5.3 (backend=QtAgg)
├☑ pooch 1.7.0
└☑ jinja2 3.1.2
Numerical (optional)
├☑ sklearn 1.3.0
├☑ numba 0.57.1
├☑ nibabel 5.1.0
├☑ nilearn 0.10.1
├☑ dipy 1.7.0
├☑ openmeeg 2.5.6
├☑ pandas 2.1.0
└☐ unavailable cupy
Visualization (optional)
├☑ pyvista 0.42.1 (OpenGL 4.6.0 Compatibility Profile Context 24.1.1.240110 via AMD Radeon(TM) Graphics)
├☑ pyvistaqt 0.0.0
├☑ vtk 9.2.6
├☑ qtpy 2.4.0 (PyQt5=5.15.4)
├☑ ipympl 0.9.3
├☑ pyqtgraph 0.13.3
├☑ mne-qt-browser 0.5.2
├☑ ipywidgets 7.7.2
├☑ trame_client 2.15.0
├☑ trame_server 2.15.0
├☑ trame_vtk 2.7.1
└☑ trame_vuetify 2.4.2