def main(regions, atlas=None, cartoon=False, debug=False, file=None):
# Set look
if cartoon:
brainrender.SHADER_STYLE = "cartoon"
# Create scene
scene = Scene(atlas=atlas)
# Add brain regions
if regions is not None and len(regions) > 0:
acts = scene.add_brain_regions(list(regions))
# Add silhouettes
if cartoon:
if isinstance(acts, list):
scene.add_silhouette(*acts)
else:
scene.add_silhouette(acts)
# Add data from file
if file is not None:
if file.endswith(".h5"):
scene.add_cells_from_file(file)
else:
try:
scene.add_from_file(file)
except Exception as e:
raise ValueError(
f"Failed to load data from file onto scene: {file}\n{e}"
)
# If debug set interactive = Off and close scene
if not debug:
interactive = True
else:
interactive = False
# Render and close
scene.render(interactive=interactive)
if debug:
scene.close()
"""
This example shows how to create a scene that has a cartoony look
(good for schematics and illustrations)
"""
import brainrender
brainrender.SHADER_STYLE = "cartoon" # gives actors a flat shading
from brainrender.scene import Scene
scene = Scene(title="cartoon look")
th = scene.add_brain_regions("TH", alpha=0.5)
# Create a black line around each actor
scene.add_silhouette(scene.root)
scene.add_silhouette(th, lw=3)
scene.render()
from brainrender.scene import Scene
scene = Scene()
# Load skull from file
skull = scene.add_from_file("Examples/example_files/skull.stl")
skull.c("ivory").alpha(1)
# Align skull and brain (scene.root)
skull_com = skull.centerOfMass()
root_com = scene.root.centerOfMass()
skull.origin(skull.centerOfMass())
skull.rotateY(90).rotateX(180)
skull.x(root_com[0] - skull_com[0])
skull.y(root_com[1] - skull_com[1])
skull.z(root_com[2] - skull_com[2])
skull.x(3500)
skull.rotateZ(-25)
skull.y(7800)
skull.scale([1300, 1500, 1200])
# Cut skull actor to show brain inside
scene.cut_actors_with_plane("sagittal", actors=skull)
# Improve looks
scene.add_silhouette(scene.root, lw=3)
scene.add_silhouette(skull, lw=3)
scene.render()
)
# Text to add
s = "BRAINRENDER"
# Specify a color for each letter
colors = makePalette(len(s), "salmon", "powderblue")
x = 0 # use to specify the position of each letter
# Add letters one at the time to color them individually
for n, letter in enumerate("BRAINRENDER"):
if "I" == letter or "N" == letter and n < 5: # make the spacing right
x += 0.6
else:
x += 1
# Add letter and silhouette to the scene
act = Text(
letter,
depth=0.5,
c=colors[n],
pos=(x, 0, 0),
justify="centered",
alpha=1,
)
scene.add_silhouette(act, lw=3)
scene.render()
# Add a ruler form the brain surface
scene.add_ruler_from_surface(p2, unit_scale=0.001)
# Add a ruler between the two regions
scene.add_actor(ruler(p1, p2, unit_scale=0.001, units="mm"))
# Cut with plane
stn = scene.add_brain_regions("STR", hemisphere="right").alpha(0.4)
scene.cut_actors_with_plane("sagittal", actors=hy)
# Fake render
scene.render(interactive=False)
# Add more regions and silhouettes
ca1 = scene.add_brain_regions("CA1", alpha=0.4)
scene.add_silhouette(ca1)
visp = scene.add_brain_regions("VISp", add_labels=False).lw(1).alpha(0.3)
scene.add_sphere_at_point(scene.atlas.get_region_CenterOfMass("VISp"),
radius=200)
p3 = scene.atlas.get_region_CenterOfMass("VISp")
scene.add_sphere_at_point(p3, radius=200)
# add labels
scene.add_actor_label(ca1, "CA1")
# Add some random stuf
scene.add_optic_cannula("VISp")
scene.add_plane("sagittal")
# final render
brainrender.SHADER_STYLE = "cartoon"
from brainrender.scene import Scene
scene = Scene(use_default_key_bindings=True, title="cut with plane")
# Add some actors
th = scene.add_brain_regions(["STR", "TH"], alpha=0.5)
# Specify position, size and orientation of the plane
pos = scene.atlas._root_midpoint
sx, sy = 15000, 15000
norm = [0, 1, 1]
plane = scene.atlas.get_plane_at_point(pos,
norm=norm,
sx=sx,
sy=sy,
color="lightblue")
# Cut
scene.cut_actors_with_plane(
plane,
close_actors=
False, # set close_actors to True close the holes left by cutting
showplane=True,
actors=scene.root,
)
scene.add_silhouette(scene.root)
scene.render(camera="top")
"""
This example shows how to cut actors in the scene using a plane
oriented along the sagittal axis
"""
import brainrender
brainrender.SHADER_STYLE = "cartoon"
from brainrender.scene import Scene
scene = Scene(title="cut with plane")
# Add some actors
th = scene.add_brain_regions(["STR", "TH"], alpha=0.5)
# Cut with plane
scene.cut_actors_with_plane(
"sagittal", showplane=False
) # Set showplane to True if you want to see the plane location
# Add a silhouette around each actor to emphasize the cut location
scene.add_silhouette(*th, lw=3)
scene.render(camera="top")
