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fix mne.viz.plot_topomap with some missing grad in a pair #8817

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Merged
larsoner merged 2 commits into from
Feb 1, 2021
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fix mne.viz.plot_topomap with some missing grad in a pair #8817

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7160528
fix mne.viz.plot_topomap with some missing grad in a pair
agramfort Feb 1, 2021
41ef8dd
update what's new
agramfort Feb 1, 2021
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2 changes: 2 additions & 0 deletions doc/changes/latest.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,8 @@ Bugs

- Fix bug with :ref:`mne make_scalp_surfaces` where ``--overwrite`` was not functional (:gh:`8800` by `Yu-Han Luo`_)

- Fix bug with :func:`mne.viz.plot_topomap` when plotting gradiometers with a missing channel in a pair (:gh:`8817` by `Alex Gramfort`_)

API changes
~~~~~~~~~~~

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13 changes: 13 additions & 0 deletions mne/viz/tests/test_topomap.py
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Expand Up @@ -557,6 +557,19 @@ def test_plot_topomap_bads():
plt.close('all')


def test_plot_topomap_bads_grad():
"""Test plotting topomap with bad gradiometer channels (gh-8802)."""
import matplotlib.pyplot as plt

@larsoner larsoner Feb 1, 2021

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No need to nest these imports anymore due to pytest infrastructure, eventually we can move these to the top. But it can be another PR since this whole file suffers from our old conventions.

data = np.random.RandomState(0).randn(203)
info = read_info(evoked_fname)
info['bads'] = ['MEG 2242']
picks = pick_types(info, meg='grad')
info = pick_info(info, picks)
assert len(info['chs']) == 203
plot_topomap(data, info, res=8)
plt.close('all')

@larsoner larsoner Feb 1, 2021

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Same here, no need to plt.close('all') at the end, it happens automatically via pytest now



def test_plot_topomap_nirs_overlap(fnirs_epochs):
"""Test plotting nirs topomap with overlapping channels (gh-7414)."""
fig = fnirs_epochs['A'].average(picks='hbo').plot_topomap()
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2 changes: 1 addition & 1 deletion mne/viz/topomap.py
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Expand Up @@ -856,7 +856,7 @@ def _plot_topomap(data, pos, vmin=None, vmax=None, cmap=None, sensors=True,
# deal with grad pairs
picks = _pair_grad_sensors(pos, topomap_coords=False)
pos = _find_topomap_coords(pos, picks=picks[::2], sphere=sphere)
data, _ = _merge_ch_data(data, ch_type, [])
data, _ = _merge_ch_data(data[picks], ch_type, [])
data = data.reshape(-1)
else:
picks = list(range(data.shape[0]))
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