def setUp(self):
self.coords1 = set(
(sin(0.1 * t), sin(0.2 * t), sin(0.3 * t)) for t in xrange(50))
self.o1 = Octree(((-1.0, 1.0), (-1.0, 1.0), (-1.0, 1.0)))
self.o1.extend((p, None) for p in self.coords1)
self.coords2 = set((sin(0.1 * t), sin(0.2 * t), sin(0.3 * t))
for t in xrange(150, 200))
self.o2 = Octree(((-1.0, 1.0), (-1.0, 1.0), (-1.0, 1.0)))
self.o2.extend((p, None) for p in self.coords2)
def test_union(self):
p = (0.236, -0.532, -0.117)
l = [c for (_, c, _) in self.o.by_distance_from_point(p)]
o1 = Octree(((-1.0, 1.0), (-1.0, 1.0), (-1.0, 1.0)))
o1.extend((p, True) for p in l[:25])
self.assertEqual(len(o1), 25)
o2 = Octree(((-1.0, 1.0), (-1.0, 1.0), (-1.0, 1.0)))
o2.extend((p, True) for p in l[25:])
self.assertEqual(len(o2), 25)
self.assertEqual(o1.simple_union(o2), self.o)
def setUp(self):
b = ((-1.0, 1.0), (-1.0, 1.0), (-1.0, 1.0))
points = [((sin(0.1*t), sin(0.2*t), sin(0.3*t)), t)
for t in range(50)]
self.o1 = Octree(b)
self.o1.extend(points)
self.o2 = octree_from_list(b, points)
def expand(points, distance):
expanded = Octree(expand_bounds(points.bounds, distance))
points_list = list(points)
d_angle = 0.2
max_angle = 0.600000001
all_norm_offsets = [(0, 0, 1)]
distance_slightly_reduced = 0.9999 * distance
for theta in [d_angle * (i + 1) for i in range(int(max_angle / d_angle))]:
sin_theta = sin(theta)
cos_theta = cos(theta)
num_phis = int(round(2 * pi * sin_theta / d_angle))
for phi in [2 * pi * j / num_phis for j in range(num_phis)]:
all_norm_offsets.append(
(sin(theta) * cos(phi), sin(theta) * sin(phi), cos(theta)))
num_points = len(points_list)
hits = 0
for i, (point, normal) in enumerate(points_list):
if i % 100 == 0:
print "%0.2f%% complete of %i hits from %i starting points" % (
(100.0 * i) / num_points, hits, i)
n = Vector(*normal)
nn = n.normalise()
a, b = nn.get_orthogonal_vectors()
for oa, ob, on in all_norm_offsets:
new_point = [
pc + on * nc * distance + oa * ac * distance +
ob * bc * distance for pc, nc, ac, bc in zip(point, n, a, b)
]
try:
points.by_distance_from_point(
new_point, distance_slightly_reduced).next()
except StopIteration:
expanded.insert(new_point, normal)
hits += 1
return expanded
def copy_point_cloud_excluding(points, excluding_points, distance):
clean_skin = Octree(points.bounds)
points_list = points.by_distance_from_point(
(0, 0, 0)
) #Points do not actually need to be ordered, perhaps they can be found more efficiently
for ignore, point, normal in points_list:
try:
excluding_points.by_distance_from_point(point, distance).next()
except StopIteration:
clean_skin.insert(point, normal)
return clean_skin
def __call__(self, roiGUI, triangle):
avoid_edges = []
for roi in roiGUI.rois:
avoid = []
for paths in roi.paths:
start = None
previous_vertex = None
for path in paths:
for point in path.points():
if start != point:#if first point != last point
vertex = point.splitmesh(self.mesh)
if previous_vertex is not None:
avoid.append(self.mesh.edges[(vertex, previous_vertex)])#Need an edge not a vertex!!
previous_vertex = vertex
if start is None:
start = point
avoid_edges.append(avoid)
#avoid_edges = roiGUI.get_avoidance_edges()
#Save the cut out mesh to a file
roughcut = self.mesh.cloneSubVol(triangle, avoid_edges)
print "Saving"
mesh.fileio.write_ply(roughcut, self.base_file + "rough.ply")
#Expand cut out mesh and save that to a file called external
minx = min([v.x for v in roughcut.vertices]) - 0.01
maxx = max([v.x for v in roughcut.vertices]) + 0.01
miny = min([v.y for v in roughcut.vertices]) - 0.01
maxy = max([v.y for v in roughcut.vertices]) + 0.01
minz = min([v.z for v in roughcut.vertices]) - 0.01
maxz = max([v.z for v in roughcut.vertices]) + 0.01
points = Octree(((minx, maxx), (miny, maxy), (minz, maxz)))
for v in roughcut.vertices:
n = v.normal()
points.insert((v.x, v.y, v.z), (n.x, n.y, n.z))
external = expand(points, MOULD_THICKNESS)
make_ply(external, self.base_file + "external", poisson_depth = POISSON_DEPTH)
make_ply(points, self.base_file + "external_base", poisson_depth = POISSON_DEPTH)
def onSelect(self, triangle, m, rois):
# XXX:
self.base_file = "blahblah"
avoid_edges = self.get_avoidance_edges(rois)
#Save the cut out mesh to a file
roughcut = m.cloneSubVol(triangle, avoid_edges)
self.controller.addMesh(roughcut, "Rough")
self.controller.parent.meshPanel.addMesh("Rough")
self.controller.parent.meshPanel.hideMesh("Skin")
return
print "Saving"
mesh.fileio.write_ply(roughcut, self.base_file + "rough.ply")
#Expand cut out mesh and save that to a file called external
minx = min([v.x for v in roughcut.vertices]) - 0.01
maxx = max([v.x for v in roughcut.vertices]) + 0.01
miny = min([v.y for v in roughcut.vertices]) - 0.01
maxy = max([v.y for v in roughcut.vertices]) + 0.01
minz = min([v.z for v in roughcut.vertices]) - 0.01
maxz = max([v.z for v in roughcut.vertices]) + 0.01
points = Octree(((minx, maxx), (miny, maxy), (minz, maxz)))
for v in roughcut.vertices:
n = v.normal()
points.insert((v.x, v.y, v.z), (n.x, n.y, n.z))
external = expand(points, MOULD_THICKNESS)
make_ply(external, self.base_file + "external", poisson_depth = POISSON_DEPTH)
make_ply(points, self.base_file + "external_base", poisson_depth = POISSON_DEPTH)
print "Done"
def setUp(self):
self.coords = set(
(sin(0.1 * t), sin(0.2 * t), sin(0.3 * t)) for t in xrange(50))
self.o = Octree(((-1.0, 1.0), (-1.0, 1.0), (-1.0, 1.0)))
self.o.extend((p, None) for p in self.coords)
def setUp(self):
self.o = Octree(((0.0, 1.0), (0.0, 1.0), (0.0, 1.0)))
self.o.insert((0.33, 0.66, 0.99), "Point one")
self.o.insert((0.12, 0.34, 0.56), "Point two")
self.o.insert((0.98, 0.76, 0.54), "Point three")
def __call__(self, outerROI, triangle):
#Create an Octree from inner surface
minx = min([v.x for v in self.inner_mesh.vertices]) - 0.01
maxx = max([v.x for v in self.inner_mesh.vertices]) + 0.01
miny = min([v.y for v in self.inner_mesh.vertices]) - 0.01
maxy = max([v.y for v in self.inner_mesh.vertices]) + 0.01
minz = min([v.z for v in self.inner_mesh.vertices]) - 0.01
maxz = max([v.z for v in self.inner_mesh.vertices]) + 0.01
points = Octree(((minx, maxx), (miny, maxy), (minz, maxz)))
for v in self.inner_mesh.vertices:
points.insert((v.x, v.y, v.z), v)
#Copy extend to inner surface
inner_avoid_edges = []
outer_avoid_edges = []
join_strip = []
for roi in outerROI.rois:
for start_outer, end_outer in zip(roi.points, roi.points[1:] +
[roi.points[0]]):
start_outer_vertex = outerROI.mesh.faces[
start_outer[3]].nearest_vertex(*start_outer[:3])
end_outer_vertex = outerROI.mesh.faces[
end_outer[3]].nearest_vertex(*end_outer[:3])
start_distance, start_coords, start_inner = points.by_distance_from_point(
(start_outer_vertex.x, start_outer_vertex.y,
start_outer_vertex.z)).next()
end_distance, end_coords, end_inner = points.by_distance_from_point(
(end_outer_vertex.x, end_outer_vertex.y,
end_outer_vertex.z)).next()
inner_strip = [
x.edge for x in self.inner_mesh.get_vertex_path(
start_inner, end_inner)
]
outer_strip = [
x.edge for x in self.outer_mesh.get_vertex_path(
start_outer_vertex, end_outer_vertex)
]
inner_avoid_edges = inner_avoid_edges + inner_strip
outer_avoid_edges = outer_avoid_edges + outer_strip
join_strip = join_strip + [
(start_inner, inner_strip, start_outer_vertex, outer_strip)
]
triangle_distance, triangle_coords, triangle_vertex_inner = points.by_distance_from_point(
triangle.vertices[0]).next()
start_triangle = triangle_vertex_inner.faces[0]
innerMesh = self.inner_mesh.cloneSubVol(start_triangle,
inner_avoid_edges)
print outer_avoid_edges
outerMesh = self.outer_mesh.cloneSubVol(triangle, outer_avoid_edges)
newMesh = mesh.Mesh()
newMesh.add_mesh(outerMesh)
newMesh.add_mesh(innerMesh, invert=True)
for current_inner, inner_strip, current_outer, outer_strip in join_strip:
inner_list = list_vertices(newMesh, current_inner, inner_strip)
outer_list = list_vertices(newMesh, current_outer, outer_strip)
while len(inner_list) > 1 or len(outer_list) > 1:
if len(outer_list) == 1 or (
len(inner_list) > 1 and
(inner_list[0] - outer_list[1]).magnitude() >
(inner_list[1] - outer_list[0]).magnitude()):
newMesh.add_face(inner_list[0], inner_list[1],
outer_list[0])
inner_list = inner_list[1:]
else:
newMesh.add_face(inner_list[0], outer_list[1],
outer_list[0])
outer_list = outer_list[1:]
for edge in newMesh.edges.values():
if edge.lface is None or edge.rface is None:
print edge
print newMesh.closed()
stlwriter = mesh.fileio.StlWriter(mesh.fileio.STL_FORMAT_BINARY)
stlwriter.write(newMesh, "Mould", self.base_file + "mould.stl")
def makepoints(t, zpositions, posX, posY, spacingX, spacingY, level):
t = t.astype(numpy.int16)
mean = (t[1:, 1:, 1:] + t[1:, 1:, :-1] + t[1:, :-1, 1:] + t[1:, :-1, :-1] +
t[:-1, 1:, 1:] + t[:-1, 1:, :-1] + t[:-1, :-1, 1:] +
t[:-1, :-1, :-1]) / 8
gz = (t[1:, 1:, 1:] + t[1:, 1:, :-1] + t[1:, :-1, 1:] + t[1:,:-1,:-1] \
- t[:-1, 1:, 1:] - t[:-1, 1:, :-1] - t[:-1, :-1, 1:] - t[:-1,:-1,:-1]) / 4
#print "gz", gz
gy = (t[1:, 1:, 1:] + t[1:, 1:, :-1] - t[1:, :-1, 1:] - t[1:,:-1,:-1] \
+ t[:-1, 1:, 1:] + t[:-1, 1:, :-1] - t[:-1, :-1, 1:] - t[:-1,:-1,:-1]) / 4
gx = (t[1:, 1:, 1:] - t[1:, 1:, :-1] + t[1:, :-1, 1:] - t[1:,:-1,:-1] \
+ t[:-1, 1:, 1:] - t[:-1, 1:, :-1] + t[:-1, :-1, 1:] - t[:-1,:-1,:-1]) / 4
#print t[:2, :2, :2]
#print mean[:1, :1, :1]
#print "gx", gx[:1, :1, :1]
#print "gy", gy[:1, :1, :1]
#print "gz", gz.dtype
#print ((posX, posX + (t.shape[0] + 1) * spacingX),(posY, posY + (t.shape[1] + 1) * spacingY),(min(zpositions),max(zpositions)))
results = Octree(
((posX, posX + (t.shape[2] + 1) * spacingX),
(posY, posY + (t.shape[1] + 1) * spacingY), (min(zpositions),
max(zpositions))))
#del t
gn = (gx**2 + gy**2 + gz**2)**0.5
nx = gx / gn
#print nx.dtype
#print gx.dtype
del gx
ny = gy / gn
del gy
nz = gz / gn
del gz
dist = (mean - level) / gn
del gn
dx = dist * nx
dy = dist * ny
dz = dist * nz
print dz.dtype
del dist
hit = numpy.logical_and(numpy.logical_and(abs(dx) < 0.5,
abs(dy) < 0.5),
abs(dz) < 0.5)
for i, j, k in zip(*hit.nonzero()):
rx = nx[i, j, k] / spacingX
ry = ny[i, j, k] / spacingY
rz = nz[i, j, k] / float(zpositions[i + 1] - zpositions[i])
rn = (rx**2 + ry**2 + rz**2)**0.5
rx = -rx / rn
ry = -ry / rn
rz = -rz / rn
#print k, dx[i, j, k], posX, spacingX, t.shape
#print posX, posX + (k + 0.5 - dx[i, j, k] / 2) * spacingX, posX + (t.shape[0] + 1) * spacingX
results.insert(
(posX + (k + 0.5 - dx[i, j, k]) * spacingX, posY +
(j + 0.5 - dy[i, j, k]) * spacingY, float(zpositions[i]) *
(0.5 + dz[i, j, k]) + float(zpositions[i + 1]) *
(0.5 - dz[i, j, k])), (rx, ry, rz))
del dx
del dy
del dz
del nx
del ny
del nz
return results
