def shift(mesh, shift):
#input shift as a vector
vertices = mesh.vertices
triangles = mesh.triangles
n = np.shape(vertices)[0]
newvertices = vertices + np.tile(shift, (n, 1))
return Mesh(newvertices, triangles, remove_duplicate_vertices=True)
def mesh_from_binary_stl(filename):
"Return a mesh from a binary stl file."
if filename.endswith('.bz2'):
f = bz2.BZ2File(filename)
else:
f = open(filename)
vertices = []
triangles = []
vertex_map = {}
f.read(80)
ntriangles = struct.unpack('<I', f.read(4))[0]
for i in range(ntriangles):
normal = tuple(struct.unpack('<fff', f.read(12)))
triangle = [None] * 3
for j in range(3):
vertex = tuple(struct.unpack('<fff', f.read(12)))
if vertex not in vertex_map:
vertices.append(vertex)
vertex_map[vertex] = len(vertices) - 1
triangle[j] = vertex_map[vertex]
triangles.append(triangle)
f.read(2)
f.close()
return Mesh(np.array(vertices), np.array(triangles, dtype=np.uint32))
def rotate_extrude(x, y, nsteps=64):
"""
Return the solid mesh formed by extruding the profile defined by the x and
y points `x` and `y` around the y axis.
.. note::
The path traced by the points `x` and `y` should go counter-clockwise,
otherwise the mesh will be inside out.
Example:
>>> # create a bipyramid
>>> m = rotate_extrude([0,1,0], [-1,0,1], nsteps=4)
"""
if len(x) != len(y):
raise Exception('`x` and `y` arrays must have the same length.')
points = np.array([x, y, np.zeros(len(x))]).transpose()
steps = np.linspace(0, 2 * np.pi, nsteps, endpoint=False)
vertices = np.vstack(
[rotate(points, angle, (0, -1, 0)) for angle in steps])
triangles = mesh_grid(
np.arange(len(vertices)).reshape(
(len(steps), len(points))).transpose()[::-1])
return Mesh(vertices, triangles, remove_duplicate_vertices=True)
def render_photon_track(self,geometry,photon_track,sz=1.0,color='wavelength'):
origin = photon_track.pos[:-1]
extent = photon_track.pos[1:]-photon_track.pos[:-1]
perp1 = np.cross(origin,extent)
perp1 = np.inner(sz/2.0/np.linalg.norm(perp1,axis=1),perp1.T).T
perp2 = np.cross(perp1,extent)
perp2 = np.inner(sz/2.0/np.linalg.norm(perp2,axis=1),perp2.T).T
verts = [perp1+perp2,-perp1+perp2,perp1-perp2,-perp1-perp2]
bot = [vert+origin for vert in verts]
top = [vert+origin+extent for vert in verts]
vertices = [origin,origin+extent,bot[0],top[0],bot[1],top[1],bot[2],top[2],bot[3],top[3]]
vertices = np.transpose(np.asarray(vertices,np.float32),(1,0,2))
triangles = np.asarray([[1, 3, 5], [1, 5, 7], [1, 7, 9], [1, 9, 3], [3, 2, 4], [5, 4, 6], [7, 6, 8], [9, 8, 2], [2, 0, 0], [4, 0, 0], [6, 0, 0], [8, 0, 0],
[1, 5, 1], [1, 7, 1], [1, 9, 1], [1, 3, 1], [3, 4, 5], [5, 6, 7], [7, 8, 9], [9, 2, 3], [2, 0, 4], [4, 0, 6], [6, 0, 8], [8, 0, 2]],
dtype=np.int32)
if color == 'wavelength':
r = np.asarray(np.interp(photon_track.wavelengths[:-1],[300,550,800],[0,0,255]),dtype=np.uint32)
g = np.asarray(np.interp(photon_track.wavelengths[:-1],[300,550,800],[0,255,0]),dtype=np.uint32)
b = np.asarray(np.interp(photon_track.wavelengths[:-1],[300,550,800],[255,0,0]),dtype=np.uint32)
colors = np.bitwise_or(b,np.bitwise_or(np.left_shift(g,8),np.left_shift(r,16)))
else:
r,g,b = color
colors = np.full_like(photon_track.wavelengths[:-1],((r<<16)|(g<<8)|b),dtype=np.uint32)
markers = [Solid(Mesh(v,triangles), vacuum, vacuum, color=c) for v,c in zip(vertices,colors)]
[geometry.add_solid(marker) for marker in markers]
def rotate(mesh, rotation_matrix):
vertices = mesh.vertices
triangles = mesh.triangles
n = np.shape(vertices)[0]
newvertices = np.empty((n, 3))
for i in range(n):
newvertices[i] = np.dot(rotation_matrix, vertices[i])
return Mesh(newvertices, triangles, remove_duplicate_vertices=True)
def linear_extrude(x1,
y1,
height,
x2=None,
y2=None,
center=None,
endcaps=True):
"""
Return the solid mesh formed by linearly extruding the polygon formed by
the x and y points `x1` and `y1` by a distance `height`. If `x2` and `y2`
are given extrude by connecting the points `x1` and `y1` to `x2` and `y2`;
this allows the creation of tapered solids. If `endcaps` is False, then
the triangles on the endcaps will be left off, and the mesh will not be
closed.
.. note::
The path traced by the points `x` and `y` should go counter-clockwise,
otherwise the mesh will be inside out.
Example:
>>> # create a hexagon prism
>>> angles = np.linspace(0, 2*np.pi, 6, endpoint=False)
>>> m = linear_extrude(np.cos(angles), np.sin(angles), 2.0)
"""
if len(x1) != len(y1):
raise Exception('`x` and `y` arrays must have the same length.')
if x2 is None:
x2 = x1
if y2 is None:
y2 = y1
if len(x2) != len(y2) or len(x2) != len(x1):
raise Exception('`x` and `y` arrays must have the same length.')
n = len(x1)
vertex_iterators = [
izip(x1, y1, repeat(-height / 2.0, n)),
izip(x2, y2, repeat(height / 2.0, n))
]
if endcaps:
vertex_iterators = [izip(repeat(0,n),repeat(0,n),repeat(-height/2.0,n))] \
+ vertex_iterators \
+ [izip(repeat(0,n),repeat(0,n),repeat(height/2.0,n))]
vertices = np.fromiter(flatten(roundrobin(*vertex_iterators)), float)
vertices = vertices.reshape((len(vertices) // 3, 3))
if center is not None:
vertices += center
triangles = mesh_grid(
np.arange(len(vertices)).reshape(
(len(x1), len(vertices) // len(x1))).transpose()[::-1])
return Mesh(vertices, triangles, remove_duplicate_vertices=True)
def convex_polygon(x, y):
"""
Return a polygon mesh in the x-y plane. `x` and `y` are the x and
y coordinates for the points in the polygon. The simple triangulation
method used here requires that the polygon be convex and the points
are specified in order.
"""
vertices = np.column_stack((x, y, np.zeros_like(x)))
# Every triangle includes
triangles = np.empty(shape=(len(vertices) - 2, 3), dtype=np.int32)
triangles[:, 0] = 0 # Every triangle includes vertex zero
triangles[:, 1] = np.arange(1, len(vertices) - 1)
triangles[:, 2] = np.arange(2, len(vertices))
return Mesh(vertices=vertices, triangles=triangles)
def build_detector(self, detector=None, volume_classifier=_default_volume_classifier):
'''
Add the meshes defined by this GDML to the detector. If detector is not
specified, a new detector will be created.
The volume_classifier should be a function that returns a classification
of the volume ('pmt','solid','omit') and kwargs passed to the Solid
constructor for that volume: material1, material2, color, surface
The different classifications have different behaviors:
'pmt' should specify channel_type in the kwargs to identify the channel, calls add_pmt
'solid' will add a normal solid to the Chroma geometry, calls add_solid
'omit' will not add the Solid to the Chroma geometry
'''
if detector is None:
detector = Detector(vacuum)
q = deque()
q.append([self.world, np.zeros(3), np.identity(3), None])
while len(q):
v, pos, rot, parent_material_ref = q.pop()
for child, c_pos, c_rot in zip(v.children, v.child_pos, v.child_rot):
c_pos = self.get_vals(c_pos) if c_pos is not None else np.zeros(3)
c_rot = self.get_vals(c_rot) if c_rot is not None else np.identity(3)
c_pos = np.matmul(c_pos,rot)+pos
x_rot = make_rotation_matrix(c_rot[0], [1, 0, 0])
y_rot = make_rotation_matrix(c_rot[1], [0, 1, 0])
z_rot = make_rotation_matrix(c_rot[2], [0, 0, 1])
c_rot = np.matmul(rot, np.matmul(x_rot, np.matmul(y_rot, z_rot))) #FIXME verify this order
q.append([child, c_pos, c_rot, v.material_ref])
m = self.get_mesh(v.solid_ref)
mesh = Mesh(m.vertices, m.faces) # convert PyMesh mesh to Chroma mesh
classification, kwargs = volume_classifier(v.name, v.material_ref, parent_material_ref)
if classification == 'pmt':
channel_type = kwargs.pop('channel_type',None)
solid = Solid(mesh, **kwargs)
detector.add_pmt(solid, displacement=pos, rotation=rot, channel_type=channel_type)
elif classification == 'solid':
solid = Solid(mesh, **kwargs)
detector.add_solid(solid, displacement=pos, rotation=rot)
elif classification == 'omit':
pass
else:
raise Exception('Unknown volume classification: '+classification)
return detector
def mesh_from_ascii_stl(filename):
"Return a mesh from an ascii stl file."
if filename.endswith('.bz2'):
f = bz2.BZ2File(filename)
else:
f = open(filename)
vertices = []
triangles = []
vertex_map = {}
while True:
line = f.readline()
if line == '':
break
if not line.strip().startswith('vertex'):
continue
triangle = [None] * 3
for i in range(3):
vertex = tuple([float(s) for s in line.strip().split()[1:]])
if vertex not in vertex_map:
vertices.append(vertex)
vertex_map[vertex] = len(vertices) - 1
triangle[i] = vertex_map[vertex]
if i < 3:
line = f.readline()
triangles.append(triangle)
f.close()
return Mesh(np.array(vertices), np.array(triangles, dtype=np.uint32))
def visit(self, node, debug=False):
"""
:param node: DAENode instance
DAENode instances and their pycollada underpinnings meet chroma here
Chroma needs sensitive detectors to have an associated surface
with detect property ...
"""
#assert node.__class__.__name__ == 'DAENode'
self.vcount += 1
if self.vcount < 10:
log.debug("visit : vcount %s node.index %s node.id %s " %
(self.vcount, node.index, node.id))
bps = list(node.boundgeom.primitives())
bpl = bps[0]
assert len(bps) == 1 and bpl.__class__.__name__ == 'BoundPolylist'
tris = bpl.triangleset()
vertices = tris._vertex
triangles = tris._vertex_index
mesh = Mesh(vertices, triangles, remove_duplicate_vertices=False)
material2, material1 = self.find_outer_inner_materials(node)
surface = self.find_surface(
node) # lookup Chroma surface corresponding to the node
if surface == None:
surfacename = "NOT SPECIFIED"
else:
surfacename = surface.name
if self.dump_node_info:
print "[NODE %05d:%s]" % (
node.index, node.lv.id
), " NTriangles=%d OuterMat=%s InnerMat=%s Surface=%s" % (len(
mesh.triangles), material2.name, material1.name, surfacename)
color = 0x33ffffff
solid = Solid(mesh, material1, material2, surface, color)
solid.node = node
#
# hmm a PMT is comprised of several volumes all of which
# have the same associated channel_id
#
channel_id = getattr(node, 'channel_id', None)
if not channel_id is None and channel_id > 0:
self.channel_count += 1 # nodes with associated non zero channel_id
self.channel_ids.add(channel_id)
self.chroma_geometry.add_pmt(solid, channel_id=channel_id)
else:
self.chroma_geometry.add_solid(solid)
pass
if debug and self.vcount % 1000 == 0:
print node.id
print self.vcount, bpl, tris, tris.material
print mesh
#print mesh.assemble()
bounds = mesh.get_bounds()
extent = bounds[1] - bounds[0]
print extent
def build_checkerboard_scene(checkers_per_side=10, squares_per_checker=50):
x = np.linspace(-5000.0, 5000.0,
checkers_per_side * squares_per_checker + 1)
y = np.linspace(-5000.0, 5000.0,
checkers_per_side * squares_per_checker + 1)
vertices = np.array(tuple(product(x, y, [0])))
triangles = []
for j in range(y.size - 1):
for i in range(x.size - 1):
triangles.append([
j * len(x) + i, (j + 1) * len(x) + i, (j + 1) * len(x) + i + 1
])
triangles.append(
[j * len(x) + i, j * len(x) + i + 1, (j + 1) * len(x) + i + 1])
checkerboard_mesh = Mesh(vertices,
triangles,
remove_duplicate_vertices=True)
checkerboard_color_line1 = take(
checkers_per_side * squares_per_checker * 2,
cycle([0] * 2 * squares_per_checker +
[0xffffff] * 2 * squares_per_checker)) * squares_per_checker
checkerboard_color_line2 = take(
checkers_per_side * squares_per_checker * 2,
cycle([0xffffff] * 2 * squares_per_checker +
[0] * 2 * squares_per_checker)) * squares_per_checker
checkerboard_color = take(
len(checkerboard_mesh.triangles),
cycle(checkerboard_color_line1 + checkerboard_color_line2))
checkerboard_surface_line1 = take(
checkers_per_side * squares_per_checker * 2,
cycle([black_surface] * 2 * squares_per_checker +
[lambertian_surface] * 2 *
squares_per_checker)) * squares_per_checker
checkerboard_surface_line2 = take(
checkers_per_side * squares_per_checker * 2,
cycle([lambertian_surface] * 2 * squares_per_checker +
[black_surface] * 2 * squares_per_checker)) * squares_per_checker
checkerboard_surface = take(
len(checkerboard_mesh.triangles),
cycle(checkerboard_surface_line1 + checkerboard_surface_line2))
checkerboard = Solid(checkerboard_mesh,
vacuum,
vacuum,
surface=checkerboard_surface,
color=checkerboard_color)
sphere1 = Solid(sphere(1000.0, nsteps=512), water, vacuum)
sphere2 = Solid(sphere(1000.0, nsteps=512),
vacuum,
vacuum,
surface=shiny_surface)
sphere3 = Solid(sphere(1000.0, nsteps=512),
vacuum,
vacuum,
surface=lambertian_surface)
checkerboard_scene = Geometry()
checkerboard_scene.add_solid(checkerboard, displacement=(0, 0, -1500.0))
checkerboard_scene.add_solid(sphere1, displacement=(2000.0, -2000.0, 0))
checkerboard_scene.add_solid(sphere2, displacement=(-2000.0, -2000.0, 0))
checkerboard_scene.add_solid(sphere3, displacement=(0.0, 2000.0, 0))
return checkerboard_scene