def get_region(self, *regions, alpha=1, color=None):
"""
Get brain regions meshes as Actors
:param regions: str with names of brain regions in the atlas
:param alpha: float
:param color: str
"""
if not regions:
return None
_color = color
actors = []
for region in regions:
if (
region not in self.lookup_df.acronym.values
and region not in self.lookup_df["id"].values
):
print(
f"The region {region} doesn't seem to belong to the atlas being used: {self.atlas_name}. Skipping"
)
continue
# Get mesh
obj_file = str(self.meshfile_from_structure(region))
mesh = load_mesh_from_file(obj_file, color=color, alpha=alpha)
# Get color
if color is None:
color = [
x / 255
for x in self._get_from_structure(region, "rgb_triplet")
]
# Make actor
actor = Actor(mesh, name=region, br_class="brain region")
actor.c(color).alpha(alpha)
actors.append(actor)
# reset color to input
color = _color
return return_list_smart(actors)
def ruler(p1, p2, unit_scale=1, units=None, s=50):
"""
Creates a ruler showing the distance between two points.
The ruler is composed of a line between the points and
a text indicating the distance.
:param p1: list, np.ndarray with coordinates of first point
:param p2: list, np.ndarray with coordinates of second point
:param unit_scale: float. To scale the units (e.g. show mm instead of µm)
:param units: str, name of unit (e.g. 'mm')
:param s: float size of text
"""
actors = []
# Make two line segments
midpoint = np.array([(x + y) / 2 for x, y in zip(p1, p2)])
gap1 = ((midpoint - p1) * 0.8) + p1
gap2 = ((midpoint - p2) * 0.8) + p2
actors.append(Line(p1, gap1, lw=200))
actors.append(Line(gap2, p2, lw=200))
# Add label
if units is None: # pragma: no cover
units = "" # pragma: no cover
dist = mag(p2 - p1) * unit_scale
label = precision(dist, 3) + " " + units
lbl = Text(label, pos=midpoint, s=s + 100, justify="center")
lbl.SetOrientation([0, 0, 180])
actors.append(lbl)
# Add spheres add end
actors.append(Sphere(p1, r=s, c=[0.3, 0.3, 0.3]))
actors.append(Sphere(p2, r=s, c=[0.3, 0.3, 0.3]))
act = Actor(merge(*actors), name="Ruler", br_class="Ruler")
act.c((0.3, 0.3, 0.3)).alpha(1).lw(2)
return act
