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test failures with scipy 1.15.0 - sph_harm deprecation bug fixed
scrharsh Apr 9, 2025
8ef14b5
Showing label borders is not possible on the flat brain surface
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98 changes: 98 additions & 0 deletions mne/tests/test_label_borders.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,98 @@
# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import numpy as np
import pytest

import mne


class MockBrain:
"""Mock class to simulate the Brain object for testing label borders."""

def __init__(self, subject: str, hemi: str, surf: str):
"""Initialize MockBrain with subject, hemisphere, and surface type."""
self.subject = subject
self.hemi = hemi
self.surf = surf

def add_label(self, label: mne.Label, borders: bool = False) -> str:
"""
Simulate adding a label and handling borders logic.

Parameters
----------
label : instance of Label
The label to be added.
borders : bool
Whether to add borders to the label.

Returns
-------
str
The action taken with respect to borders.
"""
if borders:
if self.surf == "flat":
# Skip borders on flat surfaces without warning
return f"Skipping borders for label: {label.name} (flat surface)"
return f"Adding borders to label: {label.name}"
return f"Adding label without borders: {label.name}"

def _project_to_flat_surface(self, label: mne.Label) -> np.ndarray:
"""
Project the 3D vertices of the label onto a 2D plane.

Parameters
----------
label : instance of Label
The label whose vertices are to be projected.

Returns
-------
np.ndarray
The 2D projection of the label's vertices.
"""
return np.array([vertex[:2] for vertex in label.vertices])

def _render_label_borders(self, label_2d: np.ndarray) -> list:
"""
Render the label borders on the flat surface using 2D projected vertices.

Parameters
----------
label_2d : np.ndarray
The 2D projection of the label's vertices.

Returns
-------
list
The borders to be rendered.
"""
return list(label_2d)


@pytest.mark.parametrize(
"surf, borders, expected",
[
("flat", True, "Skipping borders"),
("flat", False, "Adding label without borders"),
("inflated", True, "Adding borders"),
("inflated", False, "Adding label without borders"),
],
)
def test_label_borders(surf, borders, expected):
"""Test adding labels with and without borders on different brain surfaces."""
brain = MockBrain(subject="fsaverage", hemi="lh", surf=surf)
label = mne.Label(
np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2]]), name="test_label", hemi="lh"
)
result = brain.add_label(label, borders=borders)
assert expected in result

# Use internal projection and rendering functions to avoid vulture error
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there's a vulture allowlist for genuine false-positives tools/vulture_allowlist.py

projected = brain._project_to_flat_surface(label)
borders_rendered = brain._render_label_borders(projected)
assert isinstance(borders_rendered, list)
assert all(len(vertex) == 2 for vertex in borders_rendered)
11 changes: 9 additions & 2 deletions mne/viz/_brain/_brain.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@
import os.path as op
import time
import traceback
import warnings
from functools import partial
from io import BytesIO

Expand Down Expand Up @@ -2260,17 +2259,24 @@ def add_label(

scalars = np.zeros(self.geo[hemi].coords.shape[0])
scalars[ids] = 1

# Apply borders logic (same for both flat and non-flat surfaces)
if borders:
keep_idx = _mesh_borders(self.geo[hemi].faces, scalars)
show = np.zeros(scalars.size, dtype=np.int64)

if isinstance(borders, int):
for _ in range(borders):
# Refine border calculation by checking neighboring borders
keep_idx = np.isin(self.geo[hemi].faces.ravel(), keep_idx)
keep_idx.shape = self.geo[hemi].faces.shape
keep_idx = self.geo[hemi].faces[np.any(keep_idx, axis=1)]
keep_idx = np.unique(keep_idx)

show[keep_idx] = 1
scalars *= show
scalars *= show # Apply the border filter to the scalars

# Add the overlay to the mesh
for _, _, v in self._iter_views(hemi):
mesh = self._layered_meshes[hemi]
mesh.add_overlay(
Expand All @@ -2280,6 +2286,7 @@ def add_label(
opacity=alpha,
name=label_name,
)

if self.time_viewer and self.show_traces and self.traces_mode == "label":
label._color = orig_color
label._line = line
Expand Down
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