def _show_prickles(surface,
length=1,
color=None,
prickles_model=None,
children=True):
va, na, ta = surface.vertices, surface.normals, surface.triangles
if not va is None and not na is None:
n = len(va)
from numpy import empty, float32, int32, arange
van = empty((2 * n, 3), float32)
van[:n, :] = va
for a in range(3):
van[n:, a] = va[:, a] + length * na[:, a]
tan = empty((n, 2), int32)
tan[:, 0] = arange(n)
tan[:, 1] = tan[:, 0] + n
from chimerax.core.models import Model
pm = Model('prickles', surface.session)
pm.set_geometry(van, None, tan)
pm.display_style = pm.Mesh
pm.color = color.uint8x4() if color else (0, 255, 0, 255)
pm.use_lighting = False
if prickles_model:
p = prickles_model
pp, sp = prickles_model.scene_position, surface.position
if not pp.is_identity() or not sp.is_identity():
(pp.inverse() * sp).transform_points(van, in_place=True)
else:
p = surface
p = prickles_model if prickles_model else surface
p.add([pm])
if children:
for d in drawing.child_drawings():
show_prickles(d, length, color, prickles_model)
def lines_model(session,
points,
line_segments,
name='vtk lines',
color=(255, 255, 255, 255)):
from chimerax.core.models import Model
m = Model(name, session)
m.set_geometry(points, None, line_segments)
m.display_style = m.Mesh
m.color = color
return m
def smoothlines(session,
models,
step_factor=0.1,
iterations=10,
replace=False):
'''
Smooth surface models consisting of lines. Each vertex is moved the fraction step_factor
towards the average position of it and its connected neighbors. This is repeated
for the specified number of iterations. A new model is created unless the replace
option is given in which case the current model is changed.
Parameters
----------
models : list Surface
The surfaces must consist of line segments.
step_factor : float
Fraction of distance to move each vertex toward average of itself and
connected neighbors. Default 0.1
iterations : integer
Number of times to repeat smoothing. Default 10.
replace : bool
Whether to replace the lines in the existing model, or make a new model.
'''
if len(models) == 0:
from chimerax.core.errors import UserError
raise UserError(
'smoothlines: No surface models specified. Only operates on mesh lines.'
)
for model in models:
ta = model.triangles
if ta is None or ta.shape[1] != 2:
from chimerax.core.errors import UserError
raise UserError('Surface model %s does not consist of lines' %
model.name)
va = model.vertices
sva = smoothed_vertices(va, ta, step_factor, iterations)
if replace:
model.set_geometry(sva, model.normals, model.triangles)
else:
from chimerax.core.models import Model
m = Model('%s smoothed' % model.name, session)
m.set_geometry(sva, model.normals, ta)
m.display_style = m.Mesh
m.color = model.color
session.models.add([m])
model.display = False
