def __init__(self, bandgap=555, origin=(0, 0, 0), size=(1, 1, 1), shape="box"):
super(Channel, self).__init__()
self.origin = np.array(origin)
self.size = np.array(size)
self.volume = 1
if shape == "box":
self.shape = Box(origin=origin, extent=np.array(origin) + np.array(size))
for coord in size:
self.volume *= coord
elif shape == "cylinder": # takes radius, length
# The following is a little workaround to convert origin, size into cylinder (radius, length) descriptors
# Axis is based on the longest direction among the size (x,y,z)
axis = np.argmax(size)
# Length is the value of the longest axis of size
length = np.amax(size)
# Radius is the average of the other two coordinates divided by two (radius, not diameter!)
radius = np.average(np.delete(size, axis)) / 2 # Div. by 2 cause what's given it's the diameter
# Cylinder volume formula
self.volume = math.pi * radius ** 2 * length
self.shape = Cylinder(radius=radius, length=length)
# For CSG first rotation then translation (assuming scaling is not needed)
if axis == 0: # Z to X Rotation needed
self.shape.append_transform(tf.rotation_matrix(math.pi / 2.0, [0, 1, 0]))
elif axis == 1: # Z to Y Rotation needed
self.shape.append_transform(tf.rotation_matrix(-math.pi / 2.0, [1, 0, 0]))
self.shape.append_transform(tf.translation_matrix(origin))
else:
self.logger.warn("The channel shape is invalid (neither box nor cylinder. It was " + str(shape))
raise Exception("Channel has invalid shape")
self.material = SimpleMaterial(bandgap)
self.name = "Channel"
def photon(self):
photon = Photon()
photon.source = self.source_id
photon.id = self.throw
self.throw += 1
# This does not work, since the area element scales with Sin(theta) d theta d phi
# See http://mathworld.wolfram.com/SpherePointPicking.html
# Reimplementing the Randomizer
phi = np.random.uniform(self.phi_min, self.phi_max)
# theta = np.random.uniform(self.theta_min, self.theta_max)
theta = -1
while theta > self.theta_max or theta < self.theta_min:
theta = np.arccos(2 * np.random.uniform(0, 1) - 1)
x = np.cos(phi) * np.sin(theta)
y = np.sin(phi) * np.sin(theta)
z = np.cos(theta)
direction = (x, y, z)
transform = tf.translation_matrix((0, 0, 0))
point = transform_point(self.center, transform)
photon.direction = direction
photon.position = point
if self.spectrum is not None:
photon.wavelength = self.spectrum.wavelength_at_probability(
np.random.uniform())
else:
photon.wavelength = self.wavelength
photon.active = True
photon.id = self.throw
self.log.debug('Emitted photon (pid: ' + str(self.throw) + ')')
self.throw += 1
return photon
def photon(self):
photon = Photon()
photon.source = self.source_id
photon.id = self.throw
self.throw += 1
# This does not work, since the area element scales with Sin(theta) d theta d phi
# See http://mathworld.wolfram.com/SpherePointPicking.html
# Reimplementing the Randomizer
phi = np.random.uniform(self.phi_min, self.phi_max)
# theta = np.random.uniform(self.theta_min, self.theta_max)
theta = -1
while theta > self.theta_max or theta < self.theta_min:
theta = np.arccos(2 * np.random.uniform(0, 1)-1)
x = np.cos(phi) * np.sin(theta)
y = np.sin(phi) * np.sin(theta)
z = np.cos(theta)
direction = (x, y, z)
transform = tf.translation_matrix((0, 0, 0))
point = transform_point(self.center, transform)
photon.direction = direction
photon.position = point
if self.spectrum is not None:
photon.wavelength = self.spectrum.wavelength_at_probability(np.random.uniform())
else:
photon.wavelength = self.wavelength
photon.active = True
photon.id = self.throw
self.log.debug('Emitted photon (pid: ' + str(self.throw)+')')
self.throw += 1
return photon
def photon(self):
photon = Photon()
photon.source = self.source_id
int_phi = np.random.randint(1, self.spacing + 1)
int_theta = np.random.randint(1, self.spacing + 1)
phi = int_phi * (self.phi_max - self.phi_min) / self.spacing
if self.theta_min == self.theta_max:
theta = self.theta_min
else:
theta = int_theta * (self.theta_max -
self.theta_min) / self.spacing
x = np.cos(phi) * np.sin(theta)
y = np.sin(phi) * np.sin(theta)
z = np.cos(theta)
direction = (x, y, z)
transform = tf.translation_matrix((0, 0, 0))
point = transform_point(self.center, transform)
photon.direction = direction
photon.position = point
if self.spectrum is not None:
photon.wavelength = self.spectrum.wavelength_at_probability(
np.random.uniform())
else:
photon.wavelength = self.wavelength
photon.active = True
photon.id = self.throw
self.log.debug('Emitted photon (pid: ' + str(self.throw) + ')')
self.throw += 1
return photon
def photon(self):
photon = Photon()
photon.source = self.source_id
photon.id = self.throw
self.throw = self.throw + 1
intphi = np.random.randint(1, self.spacing + 1)
inttheta = np.random.randint(1, self.spacing + 1)
phi = intphi * (self.phimax - self.phimin) / self.spacing
if self.thetamin == self.thetamax:
theta = self.thetamin
else:
theta = inttheta * (self.thetamax - self.thetamin) / self.spacing
x = np.cos(phi) * np.sin(theta)
y = np.sin(phi) * np.sin(theta)
z = np.cos(theta)
direction = (x, y, z)
transform = tf.translation_matrix((0, 0, 0))
point = transform_point(self.center, transform)
photon.direction = direction
photon.position = point
if self.spectrum != None:
photon.wavelength = self.spectrum.wavelength_at_probability(
np.random.uniform())
else:
photon.wavelength = self.wavelength
photon.active = True
return photon
def photon(self):
photon = Photon()
photon.source = self.source_id
int_phi = np.random.randint(1, self.spacing + 1)
int_theta = np.random.randint(1, self.spacing + 1)
phi = int_phi * (self.phi_max - self.phi_min) / self.spacing
if self.theta_min == self.theta_max:
theta = self.theta_min
else:
theta = int_theta * (self.theta_max - self.theta_min) / self.spacing
x = np.cos(phi) * np.sin(theta)
y = np.sin(phi) * np.sin(theta)
z = np.cos(theta)
direction = (x, y, z)
transform = tf.translation_matrix((0, 0, 0))
point = transform_point(self.center, transform)
photon.direction = direction
photon.position = point
if self.spectrum is not None:
photon.wavelength = self.spectrum.wavelength_at_probability(np.random.uniform())
else:
photon.wavelength = self.wavelength
photon.active = True
photon.id = self.throw
self.log.debug('Emitted photon (pid: ' + str(self.throw)+')')
self.throw += 1
return photon
fluro_red = Material(absorption_data=abs, emission_data=ems, quantum_efficiency=0.95, refractive_index=1.5) # 4) Give the material a linear background absorption (pmma) abs = Spectrum([0,1000], [2,2]) ems = Spectrum([0,1000], [0,0]) pmma = Material(absorption_data=abs, emission_data=ems, quantum_efficiency=0.0, refractive_index=1.5) # 5) Make the LSC and give it both dye and pmma materials #lsc = LSC(origin=(0,0,0), size=(L,W,H) ) #lsc.material = CompositeMaterial([pmma, fluro_red], refractive_index = 1.5) #lsc.name = "LSC" lsc = Rod(radius = L, length = H) lsc.material = CompositeMaterial([pmma, fluro_red], refractive_index = 1.5) lsc.name = "LSC" lsc.shape.append_transform(tf.translation_matrix((2*L,0,0))) lsc2 = Rod(radius = L, length = H) lsc2.material = CompositeMaterial([pmma, fluro_red], refractive_index = 1.5) lsc2.name = "LSC2" scene = Scene() scene.add_object(lsc2) scene.add_object(lsc) # Ask python that the directory of this script file is and use it as the location of the database file pwd = os.getcwd() sql_file = str(x) + 'homogen_db2.sql' dbfile = os.path.join(pwd, sql_file) # <--- the name of the database file trace = Tracer(scene=scene, source=source, seed=1, throws=1000, database_file=dbfile, use_visualiser=False, show_log=False)
def __init__(self, finiteplane, origin=(0., 0., 0.,)):
super(Detector, self).__init__()
self.shape = finiteplane
self.shape.append_transform(tf.translation_matrix(origin))
self.name = "cell"
self.material = None
def translate(self, translation):
self.shape.append_transform(tf.translation_matrix(translation))
def translate(self, translation):
self.shape.append_transform(tf.translation_matrix(translation))
def intersection(self, ray):
"""
Returns all forward intersection points with ray and the capped cylinder.
The intersection algoithm is taken from, "Intersecting a Ray with a Cylinder"
Joseph M. Cychosz and Warren N. Waggenspack, Jr., in "Graphics Gems IV",
Academic Press, 1994.
"""
"""
>>> cld = Cylinder(1.0, 1.0)
>>> cld.intersection(Ray([0.0, 0.0, 0.5], [1, 0, 0]))
[array([ 1. , 0. , 0.5])]
>>> cld.intersection(Ray([-5, 0.0, 0.5], [1, 0, 0]))
[array([-1. , 0. , 0.5]), array([ 1. , 0. , 0.5])]
>>> cld.intersection(Ray([.5, .5, -1], [0, 0, 1]))
[array([ 0.5, 0.5, 1. ]), array([ 0.5, 0.5, 0. ])]
>>> cld.intersection( Ray([0.0, 0.0, 2.0], [0, 0, -1]))
[array([ 0., 0., 1.]), array([ 0., 0., 0.])]
>>> cld.intersection(Ray([-0.2, 1.2, 0.5], [0.75498586, -0.53837322, 0.37436697]))
[array([ 0.08561878, 0.99632797, 0.64162681]), array([ 0.80834999, 0.48095523, 1. ])]
>>> cld.intersection(Ray(position=[ 0.65993112596983427575736414, -0.036309587083015459896273569, 1.], direction=[0.24273873128664008591570678, -0.81399482405912471083553328, 0.52772183462341881732271531]))
[array([ 0.65993113, -0.03630959, 1. ])]
>>> cld.transform = tf.translation_matrix([0,0,1])
>>> cld.intersection(Ray([-5,0.0,1.5], [1,0,0]))
[array([-1. , 0. , 1.5]), array([ 1. , 0. , 1.5])]
>>> cld.transform = tf.identity_matrix()
>>> cld.transform = tf.rotation_matrix(0.25*np.pi, [1,0,0])
>>> cld.intersection(Ray([-5,-.5,-0.25], [1,0,0]))
[array([-0.84779125, -0.5 , -0.25 ]), array([ 0.84779125, -0.5 , -0.25 ])]
"""
# Inverse transform the ray to get it into the cylinders local frame
inv_transform = tf.inverse_matrix(self.transform)
rpos = transform_point(ray.position, inv_transform)
rdir = transform_direction(ray.direction, inv_transform)
direction = np.array([0, 0, 1])
normal = np.cross(rdir, direction)
normal_magnitude = magnitude(normal)
# print normal_magnitude, "Normal magnitude"
if cmp_floats(normal_magnitude, .0):
# Ray parallel to cylinder direction
normal = norm(normal)
# d = abs(np.dot(rpos, direction))
# D = rpos - d * np.array(direction)
# if magnitude(D) <= self.radius:
# Axis aligned ray inside the cylinder volume only hits caps
# print "Inside axis aligned ray only hits caps"
bottom = Plane()
top = Plane()
top.transform = tf.translation_matrix([0, 0, self.length])
p0 = top.intersection(Ray(rpos, rdir))
p1 = bottom.intersection(Ray(rpos, rdir))
cap_intersections = []
if p0 is not None:
cap_intersections.append(p0)
if p1 is not None:
cap_intersections.append(p1)
points = []
for point in cap_intersections:
if point[0] is not None:
point = point[0]
point_radius = np.sqrt(point[0] ** 2 + point[1] ** 2)
if point_radius <= self.radius:
# print "Hit cap at point:"
# print point
# print ""
points.append(point)
if len(points) > 0:
world_points = []
for pt in points:
world_points.append(transform_point(pt, self.transform))
# print "Local points", points
# print "World points", world_points
return world_points
return None
# finish axis parallel branch
# print "Not parallel to cylinder axis."
# print ""
normal = norm(normal)
d = abs(np.dot(rpos, normal))
if d <= self.radius:
# Hit quadratic surface
O = np.cross(rpos, direction)
t = - np.dot(O, normal) / normal_magnitude
O = np.cross(normal, direction)
O = norm(O)
s = abs(np.sqrt(self.radius ** 2 - d ** 2) / np.dot(rdir, O))
t0 = t - s
p0 = rpos + t0 * rdir
t1 = t + s
p1 = rpos + t1 * rdir
points = []
if (t0 >= 0.0) and (.0 <= p0[2] <= self.length):
points.append(p0)
if (t1 >= 0.0) and (.0 <= p1[2] <= self.length):
points.append(p1)
# print "Hits quadratic surface with t0 and t1, ", t0, t1
# print ""
# print "Intersection points:"
# p0 = rpos + t0 * rdir
# p1 = rpos + t1 * rdir
# Check that hit quadratic surface in the length range
# points = []
# if (.0 <= p0[2] <= self.length) and not Ray(rpos, rdir).behind(p0):
# points.append(p0)
#
# if (.0 <= p1[2] <= self.length) and not Ray(rpos, rdir).behind(p1):
# points.append(p1)
# print points
# Now compute intersection with end caps
# print "Now to calculate caps intersections"
bottom = Plane()
top = Plane()
top.transform = tf.translation_matrix([0, 0, self.length])
p2 = top.intersection(Ray(rpos, rdir))
p3 = bottom.intersection(Ray(rpos, rdir))
cap_intersections = []
if p2 is not None:
cap_intersections.append(p2)
if p3 is not None:
cap_intersections.append(p3)
for point in cap_intersections:
if point[0] is not None:
point = point[0]
point_radius = np.sqrt(point[0] ** 2 + point[1] ** 2)
if point_radius <= self.radius:
# print "Hit cap at point:"
# print point
# print ""
points.append(point)
# print points
if len(points) > 0:
world_points = []
for pt in points:
world_points.append(transform_point(pt, self.transform))
return world_points
return None