Description of the problem
raw.get_data() returns all channels (including bad channels) by default.
spectrum.get_data() returns only good channels by default. This is inconsistent and therefore confusing. I just spent hours understanding why the indices in spectrum.ch_names don't match the data indices in spectrum.get_data().
Steps to reproduce
import mne
from mne import create_info
from mne.io import RawArray
from numpy.random import default_rng
def create_toy_data(n_channels=2, duration=25, sfreq=250, seed=None):
rng = default_rng(seed)
data = rng.standard_normal(size=(n_channels, 50 * sfreq)) * 5e-6
info = create_info(n_channels, sfreq, "eeg")
return RawArray(data, info)
raw = create_toy_data()
raw.info["bads"] = ['0']
spectrum = raw.compute_psd(picks=raw.ch_names, verbose=False)
assert len(spectrum.get_data()) == len(raw.get_data()), "spectrum.get_data() should return bad channels as raw.get_data() does."
---------------------------------------------------------------------------
AssertionError Traceback (most recent call last)
Cell In [22], line 1
----> 1 assert len(spectrum.get_data()) == len(spectrum.ch_names), "spectrum.get_data() should return bad channels as raw.get_data() does."
AssertionError: spectrum.get_data() should return bad channels as raw.get_data() does.Link to data
No response
Expected results
I would suggest to return all channels by default in both cases. I plotted my channels by looping over spectrum.get_data()[index] and using the label=spectrum.ch_names[index]. I could imagine that more people plan to do this as it is really important to plot the PSD of bad channels to check whether they are actually bad.
len(spectrum.get_data()) != len(spectrum.ch_names) is not intuitive in my opinion.
Actual results
inconsistent_get_data.pdf
Additional information
Platform: macOS-12.6.1-arm64-arm-64bit
Python: 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:41:22) [Clang 13.0.1 ]
Executable: /Users/moritzgerster/anaconda3/envs/bids_neu/bin/python
CPU: arm: 10 cores
Memory: 16.0 GB
mne: 1.2.2
numpy: 1.23.4 {OpenBLAS 0.3.21 with 10 threads}
scipy: 1.9.3
matplotlib: 3.6.2 {backend=module://matplotlib_inline.backend_inline}
sklearn: 1.1.3
numba: 0.56.3
nibabel: 4.0.2
nilearn: 0.9.2
dipy: 1.5.0
openmeeg: Not found
cupy: Not found
pandas: 1.5.1
pyvista: 0.37.0 {OpenGL 4.1 Metal - 76.3 via Apple M1 Pro}
pyvistaqt: 0.9.0
ipyvtklink: 0.2.2
vtk: 9.2.2
qtpy: 2.3.0 {PyQt5=5.15.6}
ipympl: Not found
pyqtgraph: 0.13.1
pooch: v1.6.0
mne_bids: 0.12.dev0
mne_nirs: Not found
mne_features: Not found
mne_qt_browser: 0.4.0
mne_connectivity: Not found
mne_icalabel: Not found
Description of the problem
raw.get_data()returns all channels (including bad channels) by default.spectrum.get_data()returns only good channels by default. This is inconsistent and therefore confusing. I just spent hours understanding why the indices inspectrum.ch_namesdon't match the data indices inspectrum.get_data().Steps to reproduce
Link to data
No response
Expected results
I would suggest to return all channels by default in both cases. I plotted my channels by looping over
spectrum.get_data()[index]and using thelabel=spectrum.ch_names[index]. I could imagine that more people plan to do this as it is really important to plot the PSD of bad channels to check whether they are actually bad.len(spectrum.get_data()) != len(spectrum.ch_names)is not intuitive in my opinion.Actual results
inconsistent_get_data.pdf
Additional information