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Cannot use evoked.animate_topomap() on CSD data #12599

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michalrzak opened this issue May 2, 2024 · 1 comment · Fixed by #12605
Closed

Cannot use evoked.animate_topomap() on CSD data #12599

michalrzak opened this issue May 2, 2024 · 1 comment · Fixed by #12605
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@michalrzak
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michalrzak commented May 2, 2024 •
edited

Description of the problem

When computing CSD from an EEG dataset, the animate_topomap method does not to run. This is most likely a bug, as plot_topomap has no such restrictions.

The problem is relatively easy to fix by just adding "csd" here.

The bigger question I suppose is why the checks in plot_tomap and animate_topomap are different and whether they should be merged to the same. This would account to changing the line here to ch_type = _get_plot_ch_type(evoked, ch_type) such as in the plot_topomap method.

Steps to reproduce

This FAILS:

import mne
from mne.datasets import sample

# load data
data_path = sample.data_path()
meg_path = data_path / "MEG" / "sample"
raw = mne.io.read_raw_fif(meg_path / "sample_audvis_raw.fif")
raw.drop_channels(raw.info["bads"])

# find events
events = mne.find_events(raw)
event_id = {
    "auditory/left": 1,
    "auditory/right": 2,
    "visual/left": 3,
    "visual/right": 4,
    "smiley": 5,
    "button": 32,
}

# only compute with eeg data
raw.pick(["eeg"])

# compute CSD
epochs = mne.Epochs(raw, events, event_id=event_id, tmin=-0.2, tmax=0.5, preload=True)
evoked = epochs["auditory"].average()
evoked_csd = mne.preprocessing.compute_current_source_density(evoked)

# animate topomap
evoked_csd.animate_topomap(times=[-0.1, 0, 0.1])

This DOES NOT fail

...

evoked_csd.plot_topomap(times=[-0.1, 0, 0.1])

Link to data

No response

Expected results

The animated topomap is shown.

Actual results

Channel type not supported. Supported channel types include 'mag', 'grad', 'eeg'. 'hbo', 'hbr', 'fnirs_cw_amplitude', and 'fnirs_od'.

Additional information

Platform             Linux-6.8.6-100.fc38.x86_64-x86_64-with-glibc2.37
Python               3.12.2 (main, Feb 21 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)]
Executable           /home/zakm00/git/auditory-stimulation-data-analysis/.venv/bin/python
CPU                   (16 cores)
Memory               15.3 GB

Core
├☒ mne               1.6.1 (outdated, release 1.7.0 is available!)
├☑ numpy             1.26.4 (unknown linalg bindings (threadpoolctl module not found: No module named 'threadpoolctl'))
├☑ scipy             1.13.0
├☑ matplotlib        3.8.3 (backend=module://matplotlib_inline.backend_inline)
├☑ pooch             1.8.1
└☑ jinja2            3.1.3

Numerical (optional)
└☐ unavailable       sklearn, numba, nibabel, nilearn, dipy, openmeeg, cupy, pandas

Visualization (optional)
├☑ pyvista           0.43.5 (OpenGL 4.6 (Core Profile) Mesa 23.1.9 via Mesa Intel(R) Graphics (ADL GT2))
├☑ pyvistaqt         0.11.0
├☑ vtk               9.3.0
├☑ qtpy              2.4.1 (PyQt6=6.6.1)
├☑ ipympl            0.9.4
├☑ pyqtgraph         0.13.6
├☑ mne-qt-browser    0.6.2
├☑ ipywidgets        8.1.2
└☐ unavailable       trame_client, trame_server, trame_vtk, trame_vuetify

Ecosystem (optional)
└☐ unavailable       mne-bids, mne-nirs, mne-features, mne-connectivity, mne-icalabel, mne-bids-pipeline

To update to the latest supported release version to get bugfixes and improvements, visit https://mne.tools/stable/install/updating.html
@michalrzak michalrzak added the BUG label May 2, 2024
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welcome bot commented May 2, 2024

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

@michalrzak michalrzak mentioned this issue May 7, 2024
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animate_topomap - CSD fix michalrzak/mne-python
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@michalrzak