Epochs.compute_psd doesn't working

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1

Hello,
Now Iā€™m using compute_psd method according to this tutorial Sleep stage classification from polysomnography (PSG) data ā€” MNE 1.6.0 documentation

And when Iā€™m using compute_psd, an error will occur like this

AttributeError: ā€˜Epochsā€™ object has no attribute ā€˜compute_psdā€™

However, I have tested ā€˜plot_psdā€™ method, and it works fine for me.

Can you please advice how to fix this thing? Thank you so much :smiley:

folder = mne.datasets.sample.data_path()
file = os.path.join(folder, 'MEG', 'sample', 'sample_audvis_raw.fif')
raw = mne.io.read_raw_fif(file, preload=True)
samf = raw.info['sfreq']

para = dict(order=3, ftype='butter', output='sos')
h_para = mne.filter.construct_iir_filter(para, f_pass=0.3, sfreq=samf, btype='high', return_copy=False)
l_para = mne.filter.construct_iir_filter(para, f_pass=35.0, sfreq=samf, btype='low', return_copy=False)
high = raw.filter(l_freq=0.3, h_freq=None, picks=None, method='iir', iir_params=h_para)
low = high.filter(l_freq=None, h_freq=35.0, picks=None, method='iir', iir_params=l_para)

n_para = mne.filter.construct_iir_filter(para, f_stop=50.0, sfreq=samf, btype='bandstop', return_copy=False)
fil = low.notch_filter(freqs=50.0, method='iir')
epochs = mne.make_fixed_length_epochs(fil, duration=30.0, overlap=1)

def eeg_power_band(epochs):
    # specific frequency bands
    FREQ_BANDS = {"delta": [0.5, 4.5],
                  "theta": [4.5, 8.5],
                  "alpha": [8.5, 11.5],
                  "sigma": [11.5, 15.5],
                  "beta": [15.5, 30]}

    spectrum = epochs.compute_psd(picks='eeg', fmin=0.5, fmax=30.)
    psds, freqs = spectrum.get_data(return_freqs=True)
    # Normalize the PSDs
    psds /= np.sum(psds, axis=-1, keepdims=True)

    X = []
    for fmin, fmax in FREQ_BANDS.values():
        psds_band = psds[:, :, (freqs >= fmin) & (freqs < fmax)].mean(axis=-1)
        X.append(psds_band.reshape(len(psds), -1))

    return np.concatenate(X, axis=1)

power = eeg_power_band(epochs)
plt.plot(power)
plt.show()

Platform: Windows 10 Home 64-bit
Python: 3.9.10
MNE: 1.2.2

2

Hi,

This indicates that youā€™re not actually running MNE 1.2 (which is the version that introduced this functionality). You can check the output of

import mne 
mne.sys_info()

to get version information,

Best wishes,
Richard

3

Hi,
Thank you for the answer.
I have already updated MNE by using pip install -U mne but when Iā€™m check the version by using mne.sys_info it shows 1.1.0.
And when Iā€™m using pip list to check the version, it shows mne version 1.2.2

How could I fix this?
Thank you

4

I donā€™t know, sounds like some confusion between virtual environments ā€¦ you should check youā€™re updating & running MNE from the same virtual environment.

Best wishes,
Richard

5

Hi @richard

Iā€™ve the same problem (ā€œAttributeError: ā€˜Epochsā€™ object has no attribute ā€˜compute_psdā€™ā€) even if my version is the 1.3.0

here the log:

mne:              1.3.0
numpy:            1.19.3 {OpenBLAS 0.3.12 with 8 threads}
scipy:            1.6.1
matplotlib:       3.4.2 {backend=Qt5Agg}

sklearn:          0.24.1
numba:            Not found
nibabel:          Not found
nilearn:          Not found
dipy:             Not found

cupy:             Not found
pandas:           1.2.3
pyvista:          Not found
pyvistaqt:        Not found
ipyvtklink:       Not found
vtk:              Not found
qtpy:             Not found
ipympl:           Not found
pyqtgraph:        Not found
pooch:            v1.6.0

mne_bids:         Not found
mne_nirs:         Not found
mne_features:     Not found
mne_qt_browser:   Not found
mne_connectivity: Not found
mne_icalabel:     Not found

Some idea to fix the issue? thanks in advance

6

Hello @BaggioMarco, are you absolutely sure the MNE youā€™re using to run your script is actually the same that produces the output you shared? How do you run your script? Could you add to your script:

import mne
print(mne.__version__)

and see which version number is being printed?

2 Likes
7

@richard after unistalling and reinstalling 3 times finally I have the method :wink: I donā€™t know what was happening

1 Like