def setUp(self):
self.cache_dir = random_tempdir('chroma_cache_test')
self.cache = Cache(self.cache_dir)
self.a = Geometry()
self.a.add_solid(Solid(box(1, 1, 1)))
self.a.add_solid(Solid(box(1, 1, 1)), displacement=(10, 10, 10))
self.a.flatten()
self.b = Geometry()
self.b.add_solid(Solid(box(2, 2, 2)))
self.b.add_solid(Solid(box(2, 2, 2)), displacement=(10, 10, 10))
self.b.add_solid(Solid(box(2, 2, 2)), displacement=(-10, -10, -10))
self.b.flatten()
def setUp(self):
self.cache_dir = random_tempdir('chroma_cache_test')
self.cache = Cache(self.cache_dir)
self.a = Geometry()
self.a.add_solid(Solid(box(1,1,1)))
self.a.add_solid(Solid(box(1,1,1)), displacement=(10,10,10))
self.a.flatten()
self.b = Geometry()
self.b.add_solid(Solid(box(2,2,2)))
self.b.add_solid(Solid(box(2,2,2)), displacement=(10,10,10))
self.b.add_solid(Solid(box(2,2,2)), displacement=(-10,-10,-10))
self.b.flatten()
def bvh_mesh(geometry, layer):
lower_bounds, upper_bounds = geometry.bvh.get_layer(layer).get_bounds()
if len(lower_bounds) == 0 or len(upper_bounds) == 0:
raise Exception('no nodes at layer %i' % layer)
dx, dy, dz = upper_bounds[0] - lower_bounds[0]
center = np.mean([upper_bounds[0],lower_bounds[0]], axis=0)
mesh = make.box(dx, dy, dz, center)
for center, dx, dy, dz in zip(np.mean([lower_bounds,upper_bounds],axis=0),
*zip(*upper_bounds-lower_bounds))[1:]:
mesh += make.box(dx,dy,dz,center)
return mesh
def build_detector():
"""Returns a cubic detector made of cubic photodetectors."""
g = Geometry(water)
for pos, dir in iter_box(nx,ny,nz,spacing):
# convert to arrays
pos, dir = np.array(pos), np.array(dir)
# we need to figure out what rotation matrix to apply to each
# photodetector so that the photosensitive surface will be facing
# `dir`.
if tuple(dir) == (0,0,1):
rotation = None
elif tuple(dir) == (0,0,-1):
rotation = make_rotation_matrix(np.pi,(1,0,0))
else:
rotation = make_rotation_matrix(np.arccos(dir.dot((0,0,1))),
np.cross(dir,(0,0,1)))
# add the photodetector
g.add_solid(build_pd(size,glass_thickness),rotation=rotation,
displacement=pos)
world = Solid(make.box(spacing*nx,spacing*ny,spacing*nz),water,vacuum,
color=0x33ffffff)
g.add_solid(world)
return g
def build_detector():
"""Returns a cubic detector made of cubic photodetectors."""
g = Geometry(water)
for pos, dir in iter_box(nx, ny, nz, spacing):
# convert to arrays
pos, dir = np.array(pos), np.array(dir)
# we need to figure out what rotation matrix to apply to each
# photodetector so that the photosensitive surface will be facing
# `dir`.
if tuple(dir) == (0, 0, 1):
rotation = None
elif tuple(dir) == (0, 0, -1):
rotation = make_rotation_matrix(np.pi, (1, 0, 0))
else:
rotation = make_rotation_matrix(np.arccos(dir.dot((0, 0, 1))),
np.cross(dir, (0, 0, 1)))
# add the photodetector
g.add_solid(build_pd(size, glass_thickness),
rotation=rotation,
displacement=pos)
world = Solid(make.box(spacing * nx, spacing * ny, spacing * nz),
water,
vacuum,
color=0x33ffffff)
g.add_solid(world)
return g
def testAbort(self):
'''Photons that hit a triangle at normal incidence should not abort.
Photons that hit a triangle at exactly normal incidence can sometimes
produce a dot product that is outside the range allowed by acos().
Trigger these with axis aligned photons in a box.
'''
# Setup geometry
cube = Geometry(vacuum)
cube.add_solid(Solid(box(100, 100, 100), vacuum, vacuum))
geo = create_geometry_from_obj(cube, update_bvh_cache=False)
# Initialize simulation (without geant4)
sim = Simulation(geo, geant4_processes=0)
# Create initial photons
nphotons = 5
pos = np.tile([0, 0, 0], (nphotons, 1)).astype(np.float32)
dir = np.tile([0, 0, 1], (nphotons, 1)).astype(np.float32)
pol = np.zeros_like(pos)
phi = np.random.uniform(0, 2 * np.pi, nphotons).astype(np.float32)
pol[:, 0] = np.cos(phi)
pol[:, 1] = np.sin(phi)
t = np.zeros(nphotons, dtype=np.float32)
wavelengths = np.empty(nphotons, np.float32)
wavelengths.fill(400.0)
photons = Photons(pos=pos,
dir=dir,
pol=pol,
t=t,
wavelengths=wavelengths)
# First make one step to check for strangeness
photons_end = sim.simulate([photons],
keep_photons_end=True,
max_steps=1).next().photons_end
print "FIRST STEP"
print photons_end.pos[0:10]
self.assertFalse(np.isnan(photons_end.pos).any())
self.assertFalse(np.isnan(photons_end.dir).any())
self.assertFalse(np.isnan(photons_end.pol).any())
self.assertFalse(np.isnan(photons_end.t).any())
self.assertFalse(np.isnan(photons_end.wavelengths).any())
# Now let it run the usual ten steps
photons_end = sim.simulate([photons],
keep_photons_end=True,
max_steps=10).next().photons_end
aborted = (photons_end.flags & (1 << 31)) > 0
print 'aborted photon fracttion: %1.1f' % (
float(count_nonzero(aborted)) / nphotons)
self.assertFalse(aborted.any())
print "LAST STEPS"
print photons_end.pos[0:10]
def bvh_mesh(geometry, layer):
lower_bounds, upper_bounds = geometry.bvh.get_layer(layer).get_bounds()
if len(lower_bounds) == 0 or len(upper_bounds) == 0:
raise Exception('no nodes at layer %i' % layer)
dx, dy, dz = upper_bounds[0] - lower_bounds[0]
center = np.mean([upper_bounds[0],lower_bounds[0]], axis=0)
geometry = Geometry()
geometry.add_solid(Solid(make.box(dx,dy,dz,center), vacuum, vacuum, color=0x33ffffff))
for center, dx, dy, dz in list(zip(np.mean([lower_bounds,upper_bounds],axis=0),
*list(zip(*upper_bounds-lower_bounds))))[1:]:
geometry.add_solid(Solid(make.box(dx,dy,dz,center), vacuum, vacuum, color=0x33ffffff))
return create_geometry_from_obj(geometry)
def setUp(self):
# Setup geometry
cube = Detector(vacuum)
cube.add_pmt(Solid(box(10.0,10,10), vacuum, vacuum, surface=r7081hqe_photocathode))
cube.set_time_dist_gaussian(1.2, -6.0, 6.0)
cube.set_charge_dist_gaussian(1.0, 0.1, 0.5, 1.5)
geo = create_geometry_from_obj(cube, update_bvh_cache=False)
self.geo = geo
self.sim = Simulation(self.geo, geant4_processes=0)
def setUp(self):
self.cache_dir = random_tempdir('chroma_cache_test')
self.cache = Cache(self.cache_dir)
self.a = Geometry()
self.a.add_solid(Solid(box(1, 1, 1)))
self.a.add_solid(Solid(box(1, 1, 1)), displacement=(10, 10, 10))
self.a.flatten()
self.b = Geometry()
self.b.add_solid(Solid(box(2, 2, 2)))
self.b.add_solid(Solid(box(2, 2, 2)), displacement=(10, 10, 10))
self.b.add_solid(Solid(box(2, 2, 2)), displacement=(-10, -10, -10))
self.b.flatten()
# c is not in cache
self.c = Geometry()
self.c.add_solid(Solid(box(2, 2, 2)))
self.c.flatten()
self.a_hash = self.a.mesh.md5()
self.b_hash = self.b.mesh.md5()
self.c_hash = self.c.mesh.md5()
self.cache.save_geometry('a', self.a)
self.cache.save_geometry('b', self.b)
def setUp(self):
self.cache_dir = random_tempdir('chroma_cache_test')
self.cache = Cache(self.cache_dir)
self.a = Geometry()
self.a.add_solid(Solid(box(1,1,1)))
self.a.add_solid(Solid(box(1,1,1)), displacement=(10,10,10))
self.a.flatten()
self.b = Geometry()
self.b.add_solid(Solid(box(2,2,2)))
self.b.add_solid(Solid(box(2,2,2)), displacement=(10,10,10))
self.b.add_solid(Solid(box(2,2,2)), displacement=(-10,-10,-10))
self.b.flatten()
# c is not in cache
self.c = Geometry()
self.c.add_solid(Solid(box(2,2,2)))
self.c.flatten()
self.a_hash = self.a.mesh.md5()
self.b_hash = self.b.mesh.md5()
self.c_hash = self.c.mesh.md5()
self.cache.save_geometry('a', self.a)
self.cache.save_geometry('b', self.b)
def setUp(self):
# Setup geometry
cube = Detector(vacuum)
cube.add_pmt(
Solid(box(10.0, 10, 10),
vacuum,
vacuum,
surface=r7081hqe_photocathode))
cube.set_time_dist_gaussian(1.2, -6.0, 6.0)
cube.set_charge_dist_gaussian(1.0, 0.1, 0.5, 1.5)
geo = create_geometry_from_obj(cube, update_bvh_cache=False)
self.geo = geo
self.sim = Simulation(self.geo, geant4_processes=0)
def testAbort(self):
'''Photons that hit a triangle at normal incidence should not abort.
Photons that hit a triangle at exactly normal incidence can sometimes
produce a dot product that is outside the range allowed by acos().
Trigger these with axis aligned photons in a box.
'''
# Setup geometry
cube = Geometry(vacuum)
cube.add_solid(Solid(box(100,100,100), vacuum, vacuum))
geo = create_geometry_from_obj(cube, update_bvh_cache=False)
sim = Simulation(geo, geant4_processes=0)
# Create initial photons
nphotons = 10000
pos = np.tile([0,0,0], (nphotons,1)).astype(np.float32)
dir = np.tile([0,0,1], (nphotons,1)).astype(np.float32)
pol = np.zeros_like(pos)
phi = np.random.uniform(0, 2*np.pi, nphotons).astype(np.float32)
pol[:,0] = np.cos(phi)
pol[:,1] = np.sin(phi)
t = np.zeros(nphotons, dtype=np.float32)
wavelengths = np.empty(nphotons, np.float32)
wavelengths.fill(400.0)
photons = Photons(pos=pos, dir=dir, pol=pol, t=t,
wavelengths=wavelengths)
# First make one step to check for strangeness
photons_end = sim.simulate([photons], keep_photons_end=True,
max_steps=1).next().photons_end
self.assertFalse(np.isnan(photons_end.pos).any())
self.assertFalse(np.isnan(photons_end.dir).any())
self.assertFalse(np.isnan(photons_end.pol).any())
self.assertFalse(np.isnan(photons_end.t).any())
self.assertFalse(np.isnan(photons_end.wavelengths).any())
# Now let it run the usual ten steps
photons_end = sim.simulate([photons], keep_photons_end=True,
max_steps=10).next().photons_end
aborted = (photons_end.flags & (1 << 31)) > 0
print 'aborted photons: %1.1f' % \
(float(count_nonzero(aborted)) / nphotons)
self.assertFalse(aborted.any())
def setUp(self):
self.cube = Geometry(water)
self.cube.add_solid(Solid(box(100,100,100), water, water))
self.geo = create_geometry_from_obj(self.cube, update_bvh_cache=False)
self.sim = Simulation(self.geo, geant4_processes=0)
nphotons = 100000
pos = np.tile([0,0,0], (nphotons,1)).astype(np.float32)
dir = np.tile([0,0,1], (nphotons,1)).astype(np.float32)
pol = np.zeros_like(pos)
phi = np.random.uniform(0, 2*np.pi, nphotons).astype(np.float32)
pol[:,0] = np.cos(phi)
pol[:,1] = np.sin(phi)
t = np.zeros(nphotons, dtype=np.float32)
wavelengths = np.empty(nphotons, np.float32)
wavelengths.fill(400.0)
self.photons = Photons(pos=pos, dir=dir, pol=pol, t=t, wavelengths=wavelengths)
def build_detector():
"""Returns a cubic detector made of cubic photodetectors."""
world_size = 1000000 # 1 km
d = Detector(ice)
#add DOMs at locations x,y,z
channel_id = 0
for x in np.arange(-500000,500001,100000):
for y in np.arange(-500000,500001,100000):
for z in np.arange(-500000,500001,100000):
d.add_pmt(build_dom(),displacement=(x,y,z),channel_id=channel_id)
channel_id += 1
world = Solid(make.box(world_size,world_size,world_size),ice,vacuum,color=0x33ffffff)
d.add_solid(world)
return d
def setUp(self):
# Setup geometry
cube = Detector(vacuum)
cube.add_pmt(
Solid(box(10.0, 10.0, 10.0),
vacuum,
vacuum,
surface=r7081hqe_photocathode))
cube.set_time_dist_gaussian(1.2, -6.0, 6.0)
cube.set_charge_dist_gaussian(1.0, 0.1, 0.5, 1.5)
geo = create_geometry_from_obj(cube,
update_bvh_cache=True,
read_bvh_cache=False)
print "Number of channels in detector: ", geo.num_channels()
self.geo = geo
self.sim = Simulation(self.geo,
geant4_processes=0,
nthreads_per_block=1,
max_blocks=1)
self.rfile = rt.TFile("output_test_detector.root", "recreate")
self.htime = rt.TH1D("htime", "Time;ns", 120, 80, 120)
self.hcharge = rt.TH1D("hcharge", "Charge;pe", 100, 0.5, 1.5)
def build(slit_width):
directory = 'stls/' #directory containing individual detector .stls
##### Generating World #####
print 'Generating world...'
size = (40,40,40) #Bounds for world box
world = Geometry(vacuum)
bounds = Solid(make.box(*size),vacuum,vacuum,color=0x33ffffff)
world.add_solid(bounds,displacement=(18,-18,10))
##### Generating Non-Special Solids #####
print 'Generating non-special solids...'
blacklist = mfunctions.get_blacklist() #Mesh read-in blacklist
tol = 0.005 #Tolerance for painting meshes using conditionals
setup_solid = Solid(make.cube(1),vacuum,vacuum,color=0xf0fc03) #origin
for filename in os.listdir(directory):
path = os.path.join(directory,filename)
tmp_mesh = mesh_from_stl(path)
mesh_no = re.findall('\d+',path)[0] #Select mesh number
if mesh_no in ['141','142']: #Angled mirrors
setup_surf, setup_col = mfunctions.mirror(mesh_no)
"""
elif mesh_no in ['161','206']: #Slit housing
setup_surf = shiny_surface
setup_col = 0x7d6b56 #grey
"""
else: #Non-optical components
setup_surf = black_surface
setup_col = 0x7d6b56 #grey
#print 'Adding solid '+mesh_no+'/249'
if mesh_no not in blacklist: #Remove blacklisted meshes from setup
setup_solid += Solid(tmp_mesh,vacuum,vacuum,surface=setup_surf,color=setup_col)
world.add_solid(setup_solid)
##### Generating Special Solids #####
print 'Generating special solids...'
"""
#Laser Absorb
laser_absorb = Solid(make.segmented_cylinder(1,0.1),vacuum,vacuum,surface=black_surface,color=0xffff00)
cap_center = np.array((18.470600,-26.771999,19.469999))
world.add_solid(laser_absorb,displacement=cap_center)
"""
#SiPM Plate
sipm_plate = Solid(mesh_from_stl(directory+'vuv_setup - Mesh 188.stl'),vacuum,vacuum,surface=black_surface,color=0xfc7f03)
rotation_matrix = mfunctions.Ry(np.arctan(0.0755832)) #Correction for SiPM plate rotation in the STL
sipm_center = np.array((18.48695,-22.89630,9.08933)) #Centre of SiPM plate
correction = sipm_center-np.matmul(rotation_matrix,sipm_center) #Off-centre rotation induces displacement, this corrects for this
world.add_solid(sipm_plate,rotation=rotation_matrix,displacement=correction+np.array((0,1,0)))
#Detector Plate/SiPM
detector = Solid(make.box(2,3,0.01),vacuum,vacuum,surface=mfunctions.get_sipm_surface(),color=0x0dff00)
world.add_solid(detector,displacement=sipm_center+np.array((0,0.8,0)))
#Closed Mirror
#mirror_surf,mirror_col = mfunctions.mirror('250')
mirror_surf = mfunctions.get_mirror_surface()
mirror_col = 0xe6ad12
closed_mirror = Solid(mesh_from_stl(directory+'vuv_setup - Mesh 250.stl'),vacuum,vacuum,surface=mirror_surf,color=mirror_col)
world.add_solid(closed_mirror,rotation=mfunctions.Ry(np.pi),displacement=np.array((18.470901,-21.916050,19.602501))+np.array((0,0,0.613293)))
#Post-Monochromator Slit Doors
basex = np.array((0.0,0.0,0.074744,0.6,0.6))#x-points for door base
basey = np.array((0.0,0.00488564,0.0800017,0.0800017,0.0))#y-points
height = 0.65
#Max slit width: 1000micron
door1 = make.linear_extrude(basex,basey,height)
door2 = make.linear_extrude(-basex,basey,height)
slit_center = mfunctions.get_center('161')
door1_solid = Solid(door1,vacuum,vacuum,surface=shiny_surface,color=0xffff00)
door2_solid = Solid(door2,vacuum,vacuum,surface=shiny_surface,color=0xffff00)
world.add_solid(door1_solid,displacement=slit_center+np.array((0.5*slit_width,-0.144076,-0.05)))
world.add_solid(door2_solid,displacement=slit_center+np.array((-0.5*slit_width,-0.144076,-0.05)))
#PMT plate
pmt_center = mfunctions.get_center('210')
pmt_center += np.array((0.4,0,0))
pmt_solid = Solid(make.segmented_cylinder(1.5,0.1),vacuum,vacuum,surface=mfunctions.get_pmt_surface(),color=0x0dff00)
world.add_solid(pmt_solid,rotation=mfunctions.Rz(np.pi/2),displacement=pmt_center)
##### Saving Geometry to File #####
config_path = open('config/geometry.pickle','wb')
cPickle.dump(world,config_path)
config_path.close()
config_path = open('config/vars.txt','wb')
config_path.write(str(slit_width)+'\n')
config_path.write('This is the config file for geometry.pickle.\nAltering this file will cause geometry.pickle to regenerate!')
config_path.close()
print 'Done.'
return world
