def visualize_obj(obj_path, *args, color="lightcoral", **kwargs):
"""
Uses brainrender to visualize a .obj file registered to the Allen CCF
:param obj_path: str, path to a .obj file
:param color: str, color of object being rendered
"""
print("Visualizing : " + obj_path)
scene = Scene(add_root=True)
scene.add_from_file(obj_path, *args, c=color, **kwargs)
return scene
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()
Note that the mouse skull and brain meshes come from different sources
so that's why they don't match perfectly.
"""
import brainrender
brainrender.SHADER_STYLE = 'cartoon'
brainrender.ROOT_ALPHA = 1
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])
