Brain GUI modernization (Phase 5)

[payamsash]

Reference issue (if any)

Phase 5 of #14042 and following #14102

What does this implement/fix?

• Adds a "Trace List" dock
• Styling ppolish for the traces and remove the legend (but kept for Jupyter)
• visibility change for the traces and their correspondence 3D glyph
• renamed "Trace" to "Atlas"

Additional information

Docs for the functions are written by Claude. Also test is written by Claude, but I made it minimal and faster.

[larsoner]

@wmvanvliet do you have time to look? If not, I can

[wmvanvliet]

I love the trace list! I would love it even more if you could name the traces.

Why did you remove the legend though? That was a useful feature and I don't remember us discussing its removal.
The traces now look too thick on my 1080p screen. I liked them better before. The sizing of the matplotlib figure is much improved.

"Set Atlas to None to see vertex and RMS traces here." <-- a bit weird message I think, because the traces work fine with an atlas selected.

[wmvanvliet]

if the new trace list is meant to replace the old legend, then the vertex numbers and MNI coordinates need to be there.

[wmvanvliet]

The text size of the trace list is a bit bigger than the size of the other text labels. It's probably better if they were the same size.

[payamsash]

I love the trace list! I would love it even more if you could name the traces.

Do you mean user-editable names? If you add key in brain.add_data, the key will be the trace name.

Why did you remove the legend though? That was a useful feature and I don't remember us discussing its removal.

It was too small text for me, also when moving the time (dashed line) it jumps to left and right, but it's easy to return it (_legend_in_figure = True), wdyt?

The traces now look too thick on my 1080p screen. I liked them better before.

agree, I will go for lw=1.8 now its 2.4

"Set Atlas to None to see vertex and RMS traces here." <-- a bit weird message I think, because the traces work fine with an atlas selected.

I see, it should be "annotations" not "atlas" in the txt, becasue when you select an annotation, traces will be gone.

if the new trace list is meant to replace the old legend, then the vertex numbers and MNI coordinates need to be there.

agree

The text size of the trace list is a bit bigger than the size of the other text labels. It's probably better if they were the same size.

agree.

P.S. I know my eyesight isn't very good :)

[payamsash]

I use this short script for testing, I thought maybe it could be also useful for you for testing (also for next phases) @wmvanvliet

import numpy as np
import mne
from mne.datasets import sample

data_path = sample.data_path()
subjects_dir = data_path / "subjects"
brain = mne.viz.Brain(
    "sample", subjects_dir=subjects_dir, hemi="lh", background="black", show=False
)
coords = brain.geo["lh"].coords

def gaussian_patch(coords, center, sigma=15.0):
    d = np.linalg.norm(coords - center, axis=1)
    return np.exp(-(d**2) / (2 * sigma**2))

times = np.linspace(0, 1, 20)
vertices = np.arange(len(coords))
temporal = gaussian_patch(coords, center=np.array([-52.0, -18.0, -8.0]))
temporal_t = temporal[:, np.newaxis] * np.exp(3 * times)[np.newaxis, :]
brain.add_data(
    temporal_t,
    hemi="lh",
    vertices=vertices,
    fmin=0.1,
    fmax=1.0,
    colormap="hot",
    key="temporal",
    smoothing_steps=5,
    time=times,
    transparent=True
)

frontal = gaussian_patch(coords, center=np.array([-38.0, 28.0, 46.0]))
frontal_t = frontal[:, np.newaxis] * (1 - np.exp(-3 * times))[np.newaxis, :]
brain.add_data(
    frontal_t,
    hemi="lh",
    vertices=vertices,
    fmin=0.1,
    fmax=0.6,
    colormap="Blues",
    alpha=0.5,
    key="frontal",
    remove_existing=False,
    smoothing_steps=5,
    time=times,
    transparent=True,
)
brain.setup_time_viewer(show_traces=True)