def add(self, *items, names=None, classes=None, **kwargs):
"""
General method to add Actors to the scene.
:param items: vedo.Mesh, Actor, (str, Path).
If str/path it should be a path to a .obj or .stl file.
Whatever the input it's turned into an instance of Actor
before adding it to the scne
:param names: names to be assigned to the Actors
:param classs: br_classes to be assigned to the Actors
:param **kwargs: parameters to be passed to the individual
loading functions (e.g. to load from file and specify the color)
"""
names = names or [None for a in items]
classes = classes or [None for a in items]
# turn items into Actors
actors = []
for item, name, _class in zip(items, listify(names), listify(classes)):
if item is None:
continue
if isinstance(item, (Mesh, Assembly)):
actors.append(Actor(item, name=name, br_class=_class))
elif pi.utils._class_name(item) == "vtkCornerAnnotation":
# Mark text actors differently because they don't behave like
# other 3d actors
actors.append(
Actor(
item,
name=name,
br_class=_class,
is_text=True,
**kwargs,
))
elif pi.utils._class_name(item) == "Volume" and not isinstance(
item, Volume):
actors.append(
Volume(item, name=name, br_class=_class, **kwargs))
elif isinstance(item, Actor):
actors.append(item)
elif isinstance(item, (str, Path)):
mesh = load_mesh_from_file(item, **kwargs)
name = name or Path(item).name
_class = _class or "from file"
actors.append(Actor(mesh, name=name, br_class=_class))
else:
raise ValueError(
f"Unrecognized argument: {item} [{pi.utils._class_name(item)}]"
)
# Add to the lists actors
self.actors.extend(actors)
return return_list_smart(actors)
def get_plane(
self,
pos=None,
norm=None,
plane=None,
sx=None,
sy=None,
color="lightgray",
alpha=0.25,
**kwargs,
):
"""
Returns a plane going through a point at pos, oriented
orthogonally to the vector norm and of width and height
sx, sy.
:param pos: 3-tuple or list with x,y,z, coords of point the plane goes through
:param norm: 3-tuple with plane's normal vector (optional)
:param sx, sy: int, width and height of the plane
:param plane: "sagittal", "horizontal", or "frontal"
:param color, alpha: plane color and transparency
"""
axes_pairs = dict(sagittal=(0, 1), horizontal=(2, 0), frontal=(2, 1))
if pos is None:
pos = self.root.centerOfMass()
try:
norm = norm or self.space.plane_normals[plane]
except KeyError: # pragma: no cover
raise ValueError( # pragma: no cover
f"Could not find normals for plane {plane}. Atlas space provides these normals: {self.space.plane_normals}" # pragma: no cover
)
# Get plane width and height
idx_pair = (
axes_pairs[plane]
if plane is not None
else axes_pairs["horizontal"]
)
bounds = self.root.bounds()
root_bounds = [
[bounds[0], bounds[1]],
[bounds[2], bounds[3]],
[bounds[4], bounds[5]],
]
wh = [float(np.diff(root_bounds[i])) for i in idx_pair]
if sx is None:
sx = wh[0]
if sy is None:
sy = wh[1]
# return plane
return Actor(
Plane(pos=pos, normal=norm, sx=sx, sy=sy, c=color, alpha=alpha),
name=f"Plane at {pos} norm: {norm}",
br_class="plane",
)
def add_actor(self, *actors, name=None, br_class=None, store=None):
"""
Add a vtk actor to the scene
:param actor:
:param store: a list to store added actors
"""
# Parse inputs to match a name and br class to each actor
actors, names, br_classes = parse_add_actors_inputs(
actors, name, br_class)
# Add actors to scene
to_return = []
for actor, name, br_class in zip(actors, names, br_classes):
for act in listify(actor):
if act is None:
continue
try:
act = Actor(act, name=name, br_class=br_class)
except Exception: # doesn't work for annotations
act.name = name
act.br_class = br_class
act._is_transformed = False
if store is None:
self.actors.append(act)
else:
store.append(act)
to_return.append(act)
return return_list_smart(to_return)
def test_neuron():
s = Scene(title="BR")
neuron = s.add(Neuron("tests/files/neuron1.swc"))
s.add(Neuron(Actor(neuron.mesh)))
s.add(Neuron(neuron.mesh))
Neuron(Sphere())
with pytest.raises(ValueError):
Neuron(1)
with pytest.raises(FileExistsError):
Neuron("tests/files/neuronsfsfs.swc")
with pytest.raises(NotImplementedError):
Neuron("tests/files/random_cells.h5")
del s
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
