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remove plotting abs as the defauls for plotting volumetric #13989

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remove plotting abs as the defauls for plotting volumetric #13989

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6191b53
remove plotting abs as the defauls for plotting volumetric
ualsbombe Jun 26, 2026
972dcd7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 26, 2026
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1 change: 1 addition & 0 deletions mne/source_estimate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2399,6 +2399,7 @@ def plot(
initial_time=None,
initial_pos=None,
verbose=None,
plot_abs=False,

@larsoner larsoner Jun 29, 2026

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Looks like cruft from an earlier implementation?

Suggested change
plot_abs=False,

):
data = self.magnitude() if self._data_ndim == 3 else self
return plot_volume_source_estimates(
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6 changes: 4 additions & 2 deletions mne/viz/_3d.py
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Expand Up @@ -2828,7 +2828,7 @@ def _click_to_cut_coords(event, params):
# We don't care about directionality, just which is which dim
codes = codes.replace("L", "R").replace("P", "A").replace("I", "S")
idx = codes.index(dict(x="R", y="A", z="S")[ax])
img_data = np.abs(_get_img_fdata(params["img_idx"]))
img_data = _get_img_fdata(params["img_idx"])
ijk = _cut_coords_to_ijk(cut_coords, params["img_idx"])
if idx == 0:
ijk[0] = np.argmax(img_data[:, ijk[1], ijk[2]])
Expand Down Expand Up @@ -2952,6 +2952,8 @@ def _plot_and_correct(*, params, cut_coords):
symmetric_cbar=True,
title="",
)
if mode == "glass_brain":
plot_kwargs["plot_abs"] = False
params["axes"].clear()
if params.get("fig_anat") is not None and plot_kwargs["colorbar"]:
params["fig_anat"]._cbar.ax.clear()
Expand Down Expand Up @@ -3184,7 +3186,7 @@ def plot_volume_source_estimates(
lx = ax_time.axvline(stc.times[time_idx], color="g")
params.update(fig=fig, ax_time=ax_time, lx=lx, axes=axes)

allow_pos_lims = mode != "glass_brain"
allow_pos_lims = True
mapdata = _process_clim(clim, colormap, transparent, stc.data, allow_pos_lims)
_separate_map(mapdata)
diverging = "pos_lims" in mapdata["clim"]
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2 changes: 1 addition & 1 deletion tutorials/inverse/50_beamformer_lcmv.py
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Expand Up @@ -253,7 +253,7 @@
# On MNI glass brain (orthoview; 2D)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

stc.plot(mode="glass_brain", clim=dict(kind="value", lims=lims), **kwargs)
stc.plot(mode="glass_brain", clim=dict(kind="value", pos_lims=lims), **kwargs)

# %%
# Volumetric rendering (3D) with vectors
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