MRG: Automatically selects EEG channels when plotting bridged electro…

…des on topomap (mne-tools#10753)

* add support for instance with more than 1 channel type

* add entry to changelog

* add notes [skip ci]

* update gh id

* fix doc

* fix sphere issue

* better

* Make docstring more concise & add See Also

Co-authored-by: Richard Höchenberger <[email protected]>

doc/changes/latest.inc

@@ -150,6 +150,8 @@ Bugs
 
 - In :class:`mne.Report`, some figures would have an undesired border added to the edges; this has now been resolved (:gh:`10730` by `Richard Höchenberger`_)
 
+- Fix selection of EEG channels and selected sphere when plotting bridged electrodes with :func:`mne.viz.plot_bridged_electrodes` (:gh:`10753` by `Mathieu Scheltienne`_)
+
 API and behavior changes
 ~~~~~~~~~~~~~~~~~~~~~~~~
 - When creating BEM surfaces via :func:`mne.bem.make_watershed_bem` and :func:`mne.bem.make_flash_bem`, the ``copy`` parameter now defaults to ``True``. This means that instead of creating symbolic links inside the FreeSurfer subject's ``bem`` folder, we now create "actual" files. This should avoid troubles when sharing files across different operating systems and file systems (:gh:`10531` by `Richard Höchenberger`_)

mne/viz/tests/test_topomap.py

@@ -22,11 +22,12 @@
 from mne.io.proj import make_eeg_average_ref_proj, Projection
 from mne.io import read_raw_fif, read_info, RawArray
 from mne.io.constants import FIFF
-from mne.io.pick import pick_info, channel_indices_by_type
+from mne.io.pick import pick_info, channel_indices_by_type, _picks_to_idx
 from mne.io.compensator import get_current_comp
 from mne.channels import (read_layout, make_dig_montage, make_standard_montage,
                           find_ch_adjacency)
 from mne.datasets import testing
+from mne.preprocessing import compute_bridged_electrodes
 from mne.time_frequency.tfr import AverageTFR
 
 from mne.viz import plot_evoked_topomap, plot_projs_topomap, topomap
@@ -730,6 +731,13 @@ def test_plot_bridged_electrodes():
     with pytest.raises(RuntimeError, match='Expected'):
         plot_bridged_electrodes(info, bridged_idx, np.zeros((5, 6, 7)))
 
+    # test with multiple channel types
+    raw = read_raw_fif(raw_fname, preload=True)
+    picks = _picks_to_idx(raw.info, "eeg")
+    raw._data[picks[0]] = raw._data[picks[1]]  # artificially bridge electrodes
+    bridged_idx, ed_matrix = compute_bridged_electrodes(raw)
+    plot_bridged_electrodes(raw.info, bridged_idx, ed_matrix)
+
 
 def test_plot_ch_adjacency():
     """Test plotting of adjacency matrix."""

mne/viz/topomap.py

@@ -2727,8 +2727,12 @@ def plot_bridged_electrodes(info, bridged_idx, ed_matrix, title=None,
     bridged_idx : list of tuple
         The indices of channels marked as bridged with each bridged
         pair stored as a tuple.
-    ed_matrix : ndarray of float, shape (n_channels, n_channels)
+        Can be generated via
+        :func:`mne.preprocessing.compute_bridged_electrodes`.
+    ed_matrix : array of float, shape (n_channels, n_channels)
         The electrical distance matrix for each pair of EEG electrodes.
+        Can be generated via
+        :func:`mne.preprocessing.compute_bridged_electrodes`.
     title : str
         A title to add to the plot.
     topomap_args : dict | None
@@ -2738,17 +2742,24 @@ def plot_bridged_electrodes(info, bridged_idx, ed_matrix, title=None,
     -------
     fig : instance of matplotlib.figure.Figure
         The topoplot figure handle.
+
+    See Also
+    --------
+    mne.preprocessing.compute_bridged_electrodes
     """
     import matplotlib.pyplot as plt
     if topomap_args is None:
         topomap_args = dict()
     else:
         topomap_args = topomap_args.copy()  # don't change original
+    picks = pick_types(info, eeg=True)
     topomap_args.setdefault('image_interp', 'nearest')
     topomap_args.setdefault('cmap', 'summer_r')
-    topomap_args.setdefault('names', info.ch_names)
+    topomap_args.setdefault('names', pick_info(info, picks).ch_names)
     topomap_args.setdefault('show_names', True)
     topomap_args.setdefault('contours', False)
+    sphere = topomap_args['sphere'] if 'sphere' in topomap_args \
+        else _check_sphere(None)
     if 'axes' not in topomap_args:
         fig, ax = plt.subplots()
         topomap_args['axes'] = ax
@@ -2757,9 +2768,6 @@ def plot_bridged_electrodes(info, bridged_idx, ed_matrix, title=None,
     # handle colorbar here instead of in plot_topomap
     colorbar = topomap_args.pop('colorbar') if \
         'colorbar' in topomap_args else True
-    # use sphere to find positions
-    sphere = topomap_args['sphere'] if 'sphere' in topomap_args else None
-    picks = pick_types(info, eeg=True)
     if ed_matrix.shape[1:] != (picks.size, picks.size):
         raise RuntimeError(
             f'Expected {(ed_matrix.shape[0], picks.size, picks.size)} '
@@ -2770,13 +2778,13 @@ def plot_bridged_electrodes(info, bridged_idx, ed_matrix, title=None,
     for epo_idx in range(ed_matrix.shape[0]):
         ed_matrix[epo_idx][tril_idx] = ed_matrix[epo_idx].T[tril_idx]
     elec_dists = np.median(np.nanmin(ed_matrix, axis=1), axis=0)
-    pos = _find_topomap_coords(info, picks, sphere=sphere)
-    im, cn = plot_topomap(elec_dists, info, **topomap_args)
+    im, cn = plot_topomap(elec_dists, pick_info(info, picks), **topomap_args)
     fig = im.figure if fig is None else fig
     # add bridged connections
     for idx0, idx1 in bridged_idx:
-        im.axes.plot([pos[idx0][0], pos[idx1][0]],
-                     [pos[idx0][1], pos[idx1][1]], color='r')
+        pos = _find_topomap_coords(info, [idx0, idx1], sphere=sphere)
+        im.axes.plot([pos[0, 0], pos[1, 0]],
+                     [pos[0, 1], pos[1, 1]], color='r')
     if title is not None:
         im.axes.set_title(title)
     if colorbar: