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Fix slicer pre-transforming the planes' center #71

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Fix slicer pre-transforming the planes' center #71

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14 changes: 9 additions & 5 deletions brainglobe_heatmap/planner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@
print_plane("Plane 0", self.slicer.plane0, blue_dark)
print_plane("Plane 1", self.slicer.plane1, pink_dark)

def show(self):
def show(self, both=True):

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brainglobe_heatmap/planner.py#L78 

Added line #L78 was not covered by tests
"""
Renders the hetamap visualization as a 3D scene in brainrender.
"""
Expand All @@ -88,15 +88,19 @@

# add slicing planes and their norms
for plane, color, alpha in zip(
(self.slicer.plane0, self.slicer.plane1),
(
(self.slicer.plane0, self.slicer.plane1)
if both
else (self.slicer.plane0,)
),
(blue_dark, pink_dark),
(0.8, 0.3),
strict=False,
):
plane_mesh = plane.to_mesh(self.scene.root)
plane_mesh.alpha(alpha).color(color)

self.scene.add(plane_mesh, transform=False)
self.scene.add(plane_mesh)

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for vector, v_color in zip(
(plane.normal, plane.u, plane.v),
(color, red_dark, green_dark),
Expand All @@ -109,12 +113,12 @@
+ np.array(vector) * self.arrow_scale,
c=v_color,
),
transform=False,
classes=plane_mesh.br_class,
)

self.scene.add(
Sphere(plane_mesh.center, r=plane_mesh.width / 125, c="k"),
transform=False,
classes=plane_mesh.br_class,
)

self.scene.render(interactive=self.interactive, zoom=self.zoom)
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1 change: 0 additions & 1 deletion brainglobe_heatmap/slicer.py
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Expand Up @@ -51,7 +51,6 @@ def __init__(
)

position = np.array(position)
position[2] = -position[2]
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@IgorTatarnikov IgorTatarnikov Jan 21, 2025 •
edited
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This line is required for sagittal slicing to work correctly. There are some underlying oddities in how brainrender handles the last spatial dimension (x in zyx representation). Without this line sagittal slices in 2D look like:

2d_heatmap_wrong_plane

This was generated by running the heatmap_2d.py example specifying the sagittal orientation. It should look something like:

2d_heamap_sagittal

I believe this is tied together with #72 and #55. I think getting rid of this line will require changes in brainrender.


if isinstance(orientation, str):
axidx = get_ax_idx(orientation)
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