def trimesh2vtk(inputobj, alphaPerCell=False):
"""Convert trimesh object to ``Actor(vtkActor)`` object."""
from vtkplotter import Actor
#colors.printc('trimesh2vtk inputobj', type(inputobj), c=3)
inputobj_type = str(type(inputobj))
if "Trimesh" in inputobj_type or "primitives" in inputobj_type:
faces = inputobj.faces
poly = buildPolyData(inputobj.vertices, faces)
tact = Actor(poly)
if inputobj.visual.kind == 'face':
trim_c = inputobj.visual.face_colors
else:
trim_c = inputobj.visual.vertex_colors
if isSequence(trim_c):
if isSequence(trim_c[0]):
trim_cc = trim_c[:, [0, 1, 2]] / 255
trim_al = trim_c[:, 3] / 255
if inputobj.visual.kind == 'face':
tact.colorCellsByArray(trim_cc, trim_al, alphaPerCell)
else:
tact.colorVerticesByArray(trim_cc, trim_al)
else:
print('trim_c not sequence?', trim_c)
return tact
elif "PointCloud" in inputobj_type:
from vtkplotter.shapes import Points
trim_cc, trim_al = 'black', 1
if hasattr(inputobj, 'vertices_color'):
trim_c = inputobj.vertices_color
if len(trim_c):
trim_cc = trim_c[:, [0, 1, 2]] / 255
trim_al = trim_c[:, 3] / 255
trim_al = np.sum(trim_al) / len(trim_al) # just the average
return Points(inputobj.vertices, r=8, c=trim_cc, alpha=trim_al)
elif "path" in inputobj_type:
from vtkplotter.shapes import Line
from vtkplotter.actors import Assembly
lines = []
for e in inputobj.entities:
#print('trimesh entity', e.to_dict())
l = Line(inputobj.vertices[e.points], c='k', lw=2)
lines.append(l)
return Assembly(lines)
return None
def add_optic_cannula(self, target_region=None, pos=None, x_offset=0, y_offset=0,
z_offset=-500, use_line=False, **kwargs):
"""
Adds a cylindrical vtk actor to scene to render optic cannulas. By default
this is a semi-transparent blue cylinder centered on the center of mass of
a specified target region and oriented vertically.
:param target_region: str, acronym of target region to extract coordinates
of implanted fiber. By defualt the fiber will be centered on the center
of mass of the target region but the offset arguments can be used to
fine tune the position. Alternative pass a 'pos' argument with XYZ coords.
:param pos: list or tuple or np.array with X,Y,Z coordinates. Must have length = 3.
:param x_offset, y_offset, z_offset: int, used to fine tune the coordinates of
the implanted cannula.
:param **kwargs: used to specify which hemisphere the cannula is and parameters
of the rendered cylinder: color, alpha, rotation axis...
"""
# Set some default kwargs
hemisphere = kwargs.pop('hemisphere', 'right')
color = kwargs.pop('color', 'powderblue')
radius = kwargs.pop('radius', 350)
alpha = kwargs.pop('alpha', .5)
# Get coordinates of brain-side face of optic cannula
if target_region is not None:
pos = self.get_region_CenterOfMass(target_region, unilateral=True, hemisphere=hemisphere)
elif pos is None:
print("No 'pos' or 'target_region' arguments were \
passed to 'add_optic_cannula', nothing to render")
return
else:
if not len(pos) == 3:
raise ValueError(f"Invalid target coordinates argument, pos: {pos}")
# Offset position
pos[0] += y_offset
pos[1] += z_offset
pos[2] += x_offset
# Get coordinates of upper face
bounds = self.root.bounds()
top = pos.copy()
top[1] = bounds[2] - 500
if not use_line:
cylinder = self.add_vtkactor(Cylinder(pos=[top, pos], c=color, r=radius, alpha=alpha, **kwargs))
else:
cylinder = self.add_vtkactor(Line(top, pos, c=color, alpha=alpha, lw=radius))
return cylinder
def add_line_at_point(self, point, replace_coord, bounds, **kwargs):
"""
Adds a line oriented on a given axis at a point
:param point:list or 1d np array with coordinates of point where crosshair is centered
:param replace_coord: index of the coordinate to replace (i.e. along which axis is the line oriented)
:param bounds: list of two floats with lower and upper bound for line, determins the extent of the line
:param kwargs: dictionary with arguments to specify how lines should look like
"""
# Get line coords
p0, p1 = point.copy(), point.copy()
p0[replace_coord] = bounds[0]
p1[replace_coord] = bounds[1]
# Get some default params
color = kwargs.pop('c', 'blackboard')
color = kwargs.pop('color', color)
lw = kwargs.pop('lw', 3)
# Create line actor
act = self.add_vtkactor(Line(p0, p1, c=color, lw=lw, **kwargs))
return act
def trimesh2vtk(inputobj, alphaPerCell=False):
"""
Convert ``Trimesh`` object to ``Actor(vtkActor)`` or ``Assembly`` object.
"""
if isSequence(inputobj):
vms = []
for ob in inputobj:
vms.append(trimesh2vtk(ob))
return vms
# print('trimesh2vtk inputobj', type(inputobj))
inputobj_type = str(type(inputobj))
if "Trimesh" in inputobj_type or "primitives" in inputobj_type:
from vtkplotter import Actor
faces = inputobj.faces
poly = buildPolyData(inputobj.vertices, faces)
tact = Actor(poly)
if inputobj.visual.kind == "face":
trim_c = inputobj.visual.face_colors
else:
trim_c = inputobj.visual.vertex_colors
if isSequence(trim_c):
if isSequence(trim_c[0]):
sameColor = len(np.unique(
trim_c, axis=0)) < 2 # all vtxs have same color
trim_c = trim_c / 255
if sameColor:
tact.c(trim_c[0, [0, 1, 2]]).alpha(trim_c[0, 3])
else:
if inputobj.visual.kind == "face":
tact.cellColors(trim_c[:, [0, 1, 2]],
mode='colors',
alpha=trim_c[:, 3],
alphaPerCell=alphaPerCell)
else:
tact.pointColors(trim_c[:, [0, 1, 2]],
mode='colors',
alpha=trim_c[3])
return tact
elif "PointCloud" in inputobj_type:
from vtkplotter.shapes import Points
trim_cc, trim_al = "black", 1
if hasattr(inputobj, "vertices_color"):
trim_c = inputobj.vertices_color
if len(trim_c):
trim_cc = trim_c[:, [0, 1, 2]] / 255
trim_al = trim_c[:, 3] / 255
trim_al = np.sum(trim_al) / len(trim_al) # just the average
return Points(inputobj.vertices, r=8, c=trim_cc, alpha=trim_al)
elif "path" in inputobj_type:
from vtkplotter.shapes import Line
from vtkplotter.actors import Assembly
lines = []
for e in inputobj.entities:
# print('trimesh entity', e.to_dict())
l = Line(inputobj.vertices[e.points], c="k", lw=2)
lines.append(l)
return Assembly(lines)
return None