mne-tools / mne-tools/mne-python
Volume plots: axis ticks are overlapping
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Description
Description of the problem
When plotting source reconstruction results on volume MRIs, the axis labels are often mangled and overlap each other both on the colorbar but also on the y-axis of the time series plot.
Furthermore, the MRI seems and colorbar seem to be shifted relative to the black background. The axis values of the MRI are shifted, too.
Steps to reproduce
import mne
from mne.beamformer import make_lcmv, apply_lcmv
sample_path = mne.datasets.sample.data_path()
data_path = sample_path / 'MEG' / 'sample'
subjects_dir = sample_path / 'subjects'
# read raw data
fname_raw = data_path / 'sample_audvis_raw.fif'
raw = mne.io.read_raw_fif(fname_raw)
raw.pick(picks=['mag', 'stim'])
# make epochs
events = mne.find_events(raw)
epochs = mne.Epochs(raw, events, event_id=[3, 4])
evoked = epochs.average()
# load the precomputed MEG forward model from disk
fname_fwd = data_path / 'sample_audvis-meg-vol-7-fwd.fif'
fwd_meg = mne.read_forward_solution(fname_fwd)
# compute covariance matrix
data_cov = mne.compute_covariance(epochs, tmin=0.0, tmax=0.15, method='empirical')
# compute beamformer, apply, and plot
filters = make_lcmv(epochs.info, fwd_meg, data_cov=data_cov, pick_ori='max-power')
stc = apply_lcmv(evoked=evoked, filters=filters)
stc.crop(-0.05, 0.15).plot(subjects_dir=subjects_dir, subject='sample', src=fwd_meg['src']);
Link to data
No response
Expected results
A pretty plot 🙂
Actual results
Additional information
This has been confirmed to happen in Jupyter notebooks and from a plain script (see MWE, run inside VSCode). Problem has been reproduced by @drammock .
This was done in a fresh conda install of the latest release, 1.8.0
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by running the provided MWE and inspect the volume source estimate's stc.crop(...).plot(...) entry point in a notebook and plain script. Compare the colorbar, time-series y-axis, MRI positioning, and axis values with the expected alignment; done means the labels no longer overlap and the plotted MRI and axes align with the black background.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100