def labels2meshes_ski(
labelimage,
labels,
spacing=[0, 0, 0],
nvoxthr=0
): # deprecated and underdeveloped: use vtk implementation instead
""""""
for label in labels:
labelmask = labelimage == label
if np.count_nonzero(labelmask) > nvoxthr:
labelmask = binary_closing(labelmask)
verts, faces = marching_cubes(labelmask, 0, spacing=spacing)
faces = correct_mesh_orientation(labelmask,
verts,
faces,
spacing=spacing,
gradient_direction='descent')
# Fancy indexing to define two vector arrays from triangle vertices
actual_verts = verts[faces]
a = actual_verts[:, 0, :] - actual_verts[:, 1, :]
b = actual_verts[:, 0, :] - actual_verts[:, 2, :]
# Find normal vectors for each face via cross product
crosses = np.cross(a, b)
normals = crosses / (np.sum(crosses**2, axis=1)**(0.5))[:,
np.newaxis]
ob = stl.Solid(name=label)
for ii, _ in enumerate(faces):
ob.add_facet(normals[ii], actual_verts[ii])
with open(str(label) + ".stl",
'w') as f: #with open("allobjects.stl", 'a') as f:
ob.write_ascii(f) #ob.write_binary(f)
f.write("\n")
def stl_from_triangles(triangles):
facets = []
for triangle in triangles:
normal = normal_from_triangle(triangle)
facet = stl.types.Facet(normal.as_list(), [
triangle[0].as_list(), triangle[1].as_list(),
triangle[2].as_list()
])
facets.append(facet)
print("{} facets".format(len(facets)))
return stl.Solid("thing", facets)
def test_solid_output_for_simple_graph(self):
def simple(x, y):
if x > 0.5 and y > 0.5:
return 2
else:
return 1
graph = ZGraph((0, 1), (0, 1), simple, 1)
top_left_front = stl.Vector3d(0, 0, 1)
top_right_front = stl.Vector3d(1, 0, 1)
top_left_back = stl.Vector3d(0, 1, 1)
top_right_back = stl.Vector3d(1, 1, 2)
bottom_left_front = stl.Vector3d(0, 0, 0)
bottom_right_front = stl.Vector3d(1, 0, 0)
bottom_left_back = stl.Vector3d(0, 1, 0)
bottom_right_back = stl.Vector3d(1, 1, 0)
top = [
stl.Facet(stl.Vector3d(0, -1 / sqrt(2), 1 / sqrt(2)),
[top_left_front, top_right_front, top_right_back]),
stl.Facet(stl.Vector3d(-1 / sqrt(2), 0, 1 / sqrt(2)),
[top_left_front, top_right_back, top_left_back]),
]
bottom = ZGraph.triangulate(stl.Vector3d(0, 0, -1),
(bottom_left_front, bottom_left_back,
bottom_right_back, bottom_right_front))
front = ZGraph.triangulate(stl.Vector3d(0, -1, 0),
(bottom_left_front, bottom_right_front,
top_right_front, top_left_front))
right = ZGraph.triangulate(stl.Vector3d(1, 0, 0),
(bottom_right_front, bottom_right_back,
top_right_back, top_right_front))
back = ZGraph.triangulate(stl.Vector3d(0, 1, 0),
(bottom_left_back, top_left_back,
top_right_back, bottom_right_back))
left = ZGraph.triangulate(stl.Vector3d(-1, 0, 0),
(bottom_left_front, top_left_front,
top_left_back, bottom_left_back))
facets = top + bottom + front + right + back + left
expected = stl.Solid("ZGraph", facets)
self.assertEqual(graph.solid_output(), expected)
def test_solid_output_for_const_graph(self):
def const_2(x, y):
return 2
graph = ZGraph((0, 1), (0, 1), const_2, 1)
top_left_front = stl.Vector3d(0, 0, 2)
top_right_front = stl.Vector3d(1, 0, 2)
top_left_back = stl.Vector3d(0, 1, 2)
top_right_back = stl.Vector3d(1, 1, 2)
bottom_left_front = stl.Vector3d(0, 0, 0)
bottom_right_front = stl.Vector3d(1, 0, 0)
bottom_left_back = stl.Vector3d(0, 1, 0)
bottom_right_back = stl.Vector3d(1, 1, 0)
top = ZGraph.triangulate(
stl.Vector3d(0, 0, 1),
(top_left_front, top_right_front, top_right_back, top_left_back))
bottom = ZGraph.triangulate(stl.Vector3d(0, 0, -1),
(bottom_left_front, bottom_left_back,
bottom_right_back, bottom_right_front))
front = ZGraph.triangulate(stl.Vector3d(0, -1, 0),
(bottom_left_front, bottom_right_front,
top_right_front, top_left_front))
right = ZGraph.triangulate(stl.Vector3d(1, 0, 0),
(bottom_right_front, bottom_right_back,
top_right_back, top_right_front))
back = ZGraph.triangulate(stl.Vector3d(0, 1, 0),
(bottom_left_back, top_left_back,
top_right_back, bottom_right_back))
left = ZGraph.triangulate(stl.Vector3d(-1, 0, 0),
(bottom_left_front, top_left_front,
top_left_back, bottom_left_back))
facets = top + bottom + front + right + back + left
expected = stl.Solid("ZGraph", facets)
self.assertEqual(graph.solid_output(), expected)
spacing = (0.03, 0.006, 0.006)
xyzOffset = (1100, 8000, 5000)
for label in labels:
labelmask = label_im == label
verts, faces = measure.marching_cubes(labelmask, 0, spacing=spacing)
faces = measure.correct_mesh_orientation(labelmask, verts, faces, spacing=spacing, gradient_direction='descent')
# from scikit_image correct_mesh_orientation
# Fancy indexing to define two vector arrays from triangle vertices
actual_verts = verts[faces]
a = actual_verts[:, 0, :] - actual_verts[:, 1, :]
b = actual_verts[:, 0, :] - actual_verts[:, 2, :]
# Find normal vectors for each face via cross product
crosses = np.cross(a, b)
normals = crosses / (np.sum(crosses ** 2, axis=1) ** (0.5))[:, np.newaxis]
ob = stl.Solid(label)
for ii,face in enumerate(faces):
ob.add_facet(normals[ii], actual_verts[ii])
with open(str(label) + ".stl", 'w') as f: #with open("allobjects.stl", 'a') as f:
ob.write_binary(f)
f.write("\n");
dims = label_im.shape
def solid_output(self):
return stl.Solid(name="ZGraph",
facets=self.__top + self.__bottom + self.__front +
self.__right + self.__back + self.__left)
normal = tuple(np.dot(m, f.normal))
vertices = []
for i in f.vertices:
vertices.append(np.dot(m, i))
facet = stl.Facet(normal, vertices)
return facet
if __name__ == '__main__':
import stl
import os
i = 0
while i < 2 * math.pi:
i += 0.1
frame = '%02f' % (i,)
door = stl.read_binary_file(open('/home/mburr/tmp/pov/door.stl.ORIG', 'rb'))
facets = []
for facet in door.facets:
facet = fix_facet(facet)
facets.append(facet)
new_door = stl.Solid('new_door_01', facets)
stl.binary.write(new_door, open('door.%s.stl' % frame, 'wb'))
os.system('stl2pov door.%s.stl' % frame)
content = open('door.pov.template').read() % {'name': 'foo'}
open('door.%s.pov' % frame, 'wb').write(content)
break
### Fault Points as python lists
fstCurve = [
bezier(p1, p2, p3, p4, t) for t in np.linspace(0, 1 - 1 / Cres, Cres)
]
scdCurve = [bezier(p4, p5, p6, p1, t) for t in np.linspace(0, 1, Cres)]
# Assemble fault points and extrude in Z-direction
points = fstCurve + scdCurve
points.reverse()
[normals, triangles] = sTri(points, depth)
## Create STL facets with normals inwarding
faces = [stl.Facet(normals[i], triangles[i]) for i in range(len(normals))]
## Create fault solid
fault = stl.Solid(fault, faces)
fs = open(filename, mode='w+')
fault.write_ascii(fs)
## Create Outer Boundary patches
# Top patch
tp = np.array([ [bBox[0][0], bBox[1][1], bBox[0][2]],\
[bBox[1][0],bBox[1][1],bBox[0][2]] ])
[tn, tt] = sTri(tp, depth)
tf = [stl.Facet(tn[i], tt[i]) for i in range(len(tt))]
top = stl.Solid(top, tf)
top.write_ascii(fs)
# Right patch
tp = np.array([ [bBox[1][0], bBox[1][1], bBox[0][2]],\
[bBox[1][0],bBox[0][1],bBox[0][2]] ])
[tn, tt] = sTri(tp, depth)