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[BUG] Fix mne.viz.Brain.add_volume_labels matrix ordering bug #11730

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merged 10 commits into from
Jun 14, 2023
Merged

[BUG] Fix mne.viz.Brain.add_volume_labels matrix ordering bug #11730

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5041584
reorient to ras [skip ci]
alexrockhill Jun 12, 2023
30d991e
update latest
alexrockhill Jun 12, 2023
45b3ca1
better solution
alexrockhill Jun 12, 2023
e367bb6
works in both test cases
alexrockhill Jun 12, 2023
dadf398
working version
alexrockhill Jun 12, 2023
d4fa1a0
style
alexrockhill Jun 12, 2023
0ada784
rerun CIs
alexrockhill Jun 12, 2023
28d4df0
FIX: Read the docs
larsoner Jun 13, 2023
6ddf170
FIX: One more
larsoner Jun 13, 2023
1d66a8d
FIX: Order
larsoner Jun 14, 2023
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1 change: 1 addition & 0 deletions doc/changes/latest.inc
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Expand Up @@ -29,6 +29,7 @@ Enhancements
Bugs
~~~~
- Extended test to highlight bug in :func:`mne.stats.permutation_t_test` (:gh:`11575` by :newcontrib:`Joshua Calder-Travis`)
- Fix bug where :meth:`mne.viz.Brain.add_volume_labels` used an incorrect orientation (:gh:`11730` by `Alex Rockhill`_)
- Fix bug with :func:`mne.forward.restrict_forward_to_label` where cortical patch information was not adjusted (:gh:`11694` by `Eric Larson`_)
- Fix bug with PySide6 compatibility (:gh:`11721` by `Eric Larson`_)
- Fix hanging interpreter with matplotlib figures using ``mne/viz/_mpl_figure.py`` in spyder console and jupyter notebooks`(:gh:`11696` by `Mathieu Scheltienne`_)
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18 changes: 11 additions & 7 deletions mne/surface.py
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Expand Up @@ -1917,6 +1917,14 @@ def _marching_cubes(image, level, smooth=0, fill_hole_size=None, use_flying_edge
f"{level.size} elements"
)

# vtkImageData indexes as slice, row, col (Z, Y, X):
# https://discourse.vtk.org/t/very-confused-about-imdata-matrix-index-order/6608/2
# We can accomplish his by requiring F continuity and raveling later.
# We also pass double as passing integer types directly can be problematic!
image = np.asfortranarray(image, dtype=float)
image_shape = image.shape
assert image.flags.f_contiguous

# fill holes
if fill_hole_size is not None:
image = image.copy() # don't modify original
Expand All @@ -1926,11 +1934,7 @@ def _marching_cubes(image, level, smooth=0, fill_hole_size=None, use_flying_edge
bin_image = binary_dilation(bin_image, iterations=fill_hole_size, mask=mask)
image[bin_image] = val

# force double as passing integer types directly can be problematic!
image_shape = image.shape
# use order='A' to automatically detect when Fortran ordering is needed
data_vtk = numpy_to_vtk(image.ravel(order="A").astype(float), deep=True)
del image
data_vtk = numpy_to_vtk(image.ravel(order="F"), deep=False)

mc = vtkDiscreteFlyingEdges3D() if use_flying_edges else vtkDiscreteMarchingCubes()
# create image
Expand Down Expand Up @@ -1978,8 +1982,8 @@ def _marching_cubes(image, level, smooth=0, fill_hole_size=None, use_flying_edge
polydata = geometry.GetOutput()
rr = vtk_to_numpy(polydata.GetPoints().GetData())
tris = vtk_to_numpy(polydata.GetPolys().GetConnectivityArray()).reshape(-1, 3)
rr = np.ascontiguousarray(rr[:, ::-1])
tris = np.ascontiguousarray(tris[:, ::-1])
rr = np.ascontiguousarray(rr)
tris = np.ascontiguousarray(tris)
out.append((rr, tris))
return out

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