diff --git a/mne/source_estimate.py b/mne/source_estimate.py index edb1ae45764..60b82522fea 100644 --- a/mne/source_estimate.py +++ b/mne/source_estimate.py @@ -2399,6 +2399,7 @@ def plot( initial_time=None, initial_pos=None, verbose=None, + plot_abs=False, ): data = self.magnitude() if self._data_ndim == 3 else self return plot_volume_source_estimates( diff --git a/mne/viz/_3d.py b/mne/viz/_3d.py index 2c5e081b8f0..bcf24cce565 100644 --- a/mne/viz/_3d.py +++ b/mne/viz/_3d.py @@ -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]]) @@ -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() @@ -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"] diff --git a/tutorials/inverse/50_beamformer_lcmv.py b/tutorials/inverse/50_beamformer_lcmv.py index bd7228fa840..ff639ee7d9d 100644 --- a/tutorials/inverse/50_beamformer_lcmv.py +++ b/tutorials/inverse/50_beamformer_lcmv.py @@ -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