def main():
"""Main function."""
args = parse_args()
syris.init(loglevel=logging.INFO, double_precision=args.double_precision)
units = q.Quantity(1, args.units)
triangles = make_cube(
).magnitude if args.input is None else read_blender_obj(args.input)
triangles = triangles * units
tr = geom.Trajectory([(0, 0, 0)] * units)
mesh = Mesh(triangles,
tr,
center=args.center,
iterations=args.supersampling)
LOG.info('Number of triangles: {}'.format(mesh.num_triangles))
shape = (args.n, args.n)
if args.pixel_size is None:
if args.input is None:
fov = 4. * units
else:
# Maximum sample size in x and y direction
max_diff = np.max(mesh.extrema[:-1, 1] - mesh.extrema[:-1, 0])
fov = max_diff
fov *= args.margin
args.pixel_size = fov / args.n
else:
fov = args.n * args.pixel_size
if args.translate is None:
translate = (fov.simplified.magnitude / 2.,
fov.simplified.magnitude / 2., 0) * q.m
else:
translate = (args.translate[0].simplified.magnitude,
args.translate[1].simplified.magnitude, 0) * q.m
LOG.info('Translation: {}'.format(translate.rescale(q.um)))
mesh.translate(translate)
mesh.rotate(args.y_rotate, geom.Y_AX)
mesh.rotate(args.x_rotate, geom.X_AX)
fmt = 'n: {}, pixel size: {}, FOV: {}'
LOG.info(
fmt.format(args.n, args.pixel_size.rescale(q.um), fov.rescale(q.um)))
st = time.time()
proj = mesh.project(shape, args.pixel_size, t=None).get()
LOG.info('Duration: {} s'.format(time.time() - st))
offset = (0, translate[1].simplified, -(fov / 2.).simplified) * q.m
if args.projection_filename is not None:
save_image(args.projection_filename, proj)
if args.compute_slice:
sl = mesh.compute_slices((1, ) + shape, args.pixel_size,
offset=offset).get()[0]
if args.slice_filename is not None:
save_image(args.slice_filename, sl)
show(sl, title='Slice at y = {}'.format(args.n / 2))
show(proj, title='Projection')
plt.show()
def make_motion(args):
syris.init()
n = 256
shape = (n, n)
energies = np.arange(5, 30, 1) * q.keV
bm, detector = make_devices(n, energies)
mb = create_sample(n, detector.pixel_size, velocity=20 * q.mm / q.s)
mb_2 = create_sample(n, detector.pixel_size, velocity=10 * q.mm / q.s)
mb.material = get_material('pmma_5_30_kev.mat')
mb_2.material = mb.material
cube = make_cube() / q.m * 30 * detector.pixel_size + 0.1 * detector.pixel_size
fov = detector.pixel_size * n
circle = make_circle().magnitude * fov / 30000 + fov / 2
tr = Trajectory(circle, velocity=10 * q.um / q.s)
glass = get_material('glass.mat')
mesh = Mesh(cube, tr, material=glass)
ex = Experiment([bm, mb, mb_2, mesh], bm, detector, 0 * q.m, energies)
for sample in ex.samples:
if sample != bm:
sample.trajectory.bind(detector.pixel_size)
if args.show_flat:
show(get_flat(shape, energies, detector, bm), title='Counts')
plt.show()
if args.conduct:
if args.output is not None and not os.path.exists(args.output):
os.makedirs(args.output, mode=0o755)
t_0 = 0 * q.s
if args.num_images:
t_1 = args.num_images / detector.camera.fps
else:
t_1 = ex.time
st = time.time()
mpl_im = None
for i, proj in enumerate(ex.make_sequence(t_0, t_1)):
image = get_host(proj)
if args.show:
if mpl_im is None:
plt.figure()
mpl_im = plt.imshow(image)
plt.show(False)
else:
mpl_im.set_data(image)
plt.draw()
if args.output:
path = os.path.join(args.output, 'projection_{:>05}.png').format(i)
scipy.misc.imsave(path, image)
print 'Maximum intensity:', image.max()
print 'Duration: {} s'.format(time.time() - st)
plt.show()
def make_complex_trajectory_sequence(args):
edge = 20
x = np.linspace(0, args.n / 2 - args.n / 4 - edge - 5, num=10)
y = z = np.zeros(x.shape)
# Move along x axis
traj_x = Trajectory(zip(x, y, z) * args.ps, velocity=args.ps / q.s, pixel_size=args.ps)
# Move along y axis
traj_y = Trajectory(zip(y, x, z) * args.ps, velocity=args.ps / q.s, pixel_size=args.ps)
# Move along both x and y axes
traj_xy = Trajectory(zip(x, x, z) * args.ps, velocity=args.ps / q.s, pixel_size=args.ps)
# Circular trajectory of the composite body rotates around the image center and with radius
# n / 4 pixels.
circle = args.n / 2 * args.ps + make_circle().magnitude * args.n / 4 * args.ps
traj_circle = Trajectory(circle, velocity=args.ps / q.s, pixel_size=args.ps)
# Make the trajectory of the circle the same duration as the simple linear one.
traj_circle = Trajectory(circle, velocity=traj_circle.length / traj_xy.length * args.ps / q.s)
# three cubes in the same height and depth, shifted only along the x axis.
traj_stationary = Trajectory([(0, 0, 0)] * args.ps)
traj_stationary_1 = Trajectory([(-2 * edge, 0, 0)] * args.ps)
traj_stationary_2 = Trajectory([(2 * edge, 0, 0)] * args.ps)
cube = make_cube() / q.m * edge * args.ps
# The cubes are elongated along y axis.
cube[::2, :] /= 3
mesh = Mesh(cube, traj_x, orientation=geom.Y_AX)
mesh_2 = Mesh(cube, traj_y, orientation=geom.Y_AX)
mesh_3 = Mesh(cube, traj_xy, orientation=geom.Y_AX)
mesh_stationary = Mesh(cube, traj_stationary, orientation=geom.Y_AX)
mesh_stationary_1 = Mesh(cube, traj_stationary_1, orientation=geom.Y_AX)
mesh_stationary_2 = Mesh(cube, traj_stationary_2, orientation=geom.Y_AX)
bodies = [mesh, mesh_2, mesh_3, mesh_stationary, mesh_stationary_1, mesh_stationary_2]
composite = CompositeBody(traj_circle, bodies=bodies, orientation=geom.Y_AX)
composite.bind_trajectory(args.ps)
total_time = composite.time
if args.t is None:
times = np.linspace(0, 1, 100)
else:
if args.t < 0 or args.t > 1:
raise ValueError('--t must be in the range [0, 1]')
times = [args.t]
im = None
for index, i in enumerate(times):
t = i * total_time
composite.clear_transformation()
composite.move(t)
p = composite.project(args.shape, args.ps).get()
if im is None:
im = show(p, title='Projection')
else:
im.set_data(p)
plt.draw()
plt.show()
def make_cube_body(n, ps, cube_edge, phase_shift=None):
fov = n * ps
triangles = make_cube().magnitude * cube_edge / 2
# Rotation around the vertical axis
points = make_circle(axis='y', overall_angle=np.pi * q.rad,
phase_shift=phase_shift).magnitude
points = points * fov / 4 + [n / 2, 0, 0] * ps
trajectory = geom.Trajectory(points, pixel_size=ps, velocity=ps / q.s)
# *orientation* aligns the object with the trajectory derivative
mesh = Mesh(triangles, trajectory, orientation=geom.Z_AX)
return mesh
def make_cube_body(n, ps, cube_edge, phase_shift=None):
fov = n * ps
triangles = make_cube().magnitude * cube_edge / 2
# Rotation around the vertical axis
points = make_circle(axis="y",
overall_angle=np.pi * q.rad,
phase_shift=phase_shift).magnitude
points = points * fov / 4 + [n // 2, 0, 0] * ps
trajectory = geom.Trajectory(points, pixel_size=ps, velocity=ps / q.s)
# *orientation* aligns the object with the trajectory derivative
mesh = Mesh(triangles, trajectory, orientation=geom.Z_AX)
return mesh
def main():
syris.init()
n = 256
shape = (n, n)
ps = 1 * q.um
fov = n * ps
triangles = make_cube().magnitude * n / 8. * ps
# Rotation around the vertical axis
points = make_circle(axis='y').magnitude * fov / 30000 + fov / 2
trajectory = geom.Trajectory(points, pixel_size=ps, velocity=10 * q.um / q.s)
# *orientation* aligns the object with the trajectory derivative
mesh = Mesh(triangles, trajectory, orientation=geom.Z_AX)
# Compute projection at the angle Pi/4
projection = mesh.project(shape, ps, t=trajectory.time / 8).get()
show(projection)
plt.show()
def main():
syris.init()
n = 256
shape = (n, n)
ps = 1 * q.um
fov = n * ps
triangles = make_cube().magnitude * n / 8. * ps
# Rotation around the vertical axis
points = make_circle(axis='y').magnitude * fov / 30000 + fov / 2
trajectory = geom.Trajectory(points,
pixel_size=ps,
velocity=10 * q.um / q.s)
# *orientation* aligns the object with the trajectory derivative
mesh = Mesh(triangles, trajectory, orientation=geom.Z_AX)
# Compute projection at the angle Pi/4
projection = mesh.project(shape, ps, t=trajectory.time / 8).get()
show(projection)
plt.show()
def main():
args = parse_args()
syris.init(device_index=0)
n = 512
shape = (n, n)
ps = 1 * q.um
x = np.linspace(0, n, num=10)
y = z = np.zeros(x.shape)
traj_x = Trajectory(zip(x, y, z) * ps, velocity=ps / q.s)
traj_y = Trajectory(zip(y, x, z) * ps, velocity=ps / q.s)
traj_xy = Trajectory(zip(n - x, x, z) * ps, velocity=ps / q.s)
mb = MetaBall(traj_x, n * ps / 16)
cube = make_cube() / q.m * 16 * ps
mesh = Mesh(cube, traj_xy)
composite = CompositeBody(traj_y, bodies=[mb, mesh])
composite.bind_trajectory(ps)
t = args.t * n * q.s
composite.move(t)
p = composite.project(shape, ps).get()
show(p, title='Projection')
plt.show()
def test_project_composite(self):
n = 64
shape = (n, n)
ps = 1 * q.um
x = np.linspace(0, n, num=10)
y = z = np.zeros(x.shape)
traj_x = Trajectory(zip(x, y, z) * ps, velocity=ps / q.s)
traj_y = Trajectory(zip(y, x, z) * ps, velocity=ps / q.s)
traj_xy = Trajectory(zip(n - x, x, z) * ps, velocity=ps / q.s)
mb = MetaBall(traj_x, n * ps / 16)
cube = make_cube() / q.m * 16 * ps / 4
mesh = Mesh(cube, traj_xy)
composite = CompositeBody(traj_y, bodies=[mb, mesh])
composite.bind_trajectory(ps)
composite.move(n / 2 * q.s)
p = composite.project(shape, ps).get()
composite.clear_transformation()
# Compute
composite.move(n / 2 * q.s)
p_separate = (mb.project(shape, ps) + mesh.project(shape, ps)).get()
np.testing.assert_almost_equal(p, p_separate)
def make_motion(args):
syris.init()
n = 256
shape = (n, n)
energies = np.arange(5, 30, 1) * q.keV
bm, detector = make_devices(n, energies)
mb = create_sample(n, detector.pixel_size, velocity=20 * q.mm / q.s)
mb_2 = create_sample(n, detector.pixel_size, velocity=10 * q.mm / q.s)
mb.material = get_material('pmma_5_30_kev.mat')
mb_2.material = mb.material
cube = make_cube(
) / q.m * 30 * detector.pixel_size + 0.1 * detector.pixel_size
fov = detector.pixel_size * n
circle = make_circle().magnitude * fov / 30000 + fov / 2
tr = Trajectory(circle, velocity=10 * q.um / q.s)
glass = get_material('glass.mat')
mesh = Mesh(cube, tr, material=glass)
ex = Experiment([bm, mb, mb_2, mesh], bm, detector, 0 * q.m, energies)
for sample in ex.samples:
if sample != bm:
sample.trajectory.bind(detector.pixel_size)
if args.show_flat:
show(get_flat(shape, energies, detector, bm), title='Counts')
plt.show()
if args.conduct:
if args.output is not None and not os.path.exists(args.output):
os.makedirs(args.output, mode=0o755)
t_0 = 0 * q.s
if args.num_images:
t_1 = args.num_images / detector.camera.fps
else:
t_1 = ex.time
st = time.time()
mpl_im = None
for i, proj in enumerate(ex.make_sequence(t_0, t_1)):
image = get_host(proj)
if args.show:
if mpl_im is None:
plt.figure()
mpl_im = plt.imshow(image)
plt.show(False)
else:
mpl_im.set_data(image)
plt.draw()
if args.output:
path = os.path.join(args.output,
'projection_{:>05}.png').format(i)
scipy.misc.imsave(path, image)
print 'Maximum intensity:', image.max()
print 'Duration: {} s'.format(time.time() - st)
plt.show()
def setUp(self):
default_syris_init()
self.triangles = make_cube()
self.trajectory = Trajectory([(0, 0, 0)] * q.m)
self.mesh = Mesh(self.triangles, self.trajectory)
def setUp(self):
syris.init(device_index=0)
self.triangles = make_cube()
self.trajectory = Trajectory([(0, 0, 0)] * q.m)
self.mesh = Mesh(self.triangles, self.trajectory)
def make_complex_trajectory_sequence(args):
edge = 20
x = np.linspace(0, args.n / 2 - args.n / 4 - edge - 5, num=10)
y = z = np.zeros(x.shape)
# Move along x axis
traj_x = Trajectory(zip(x, y, z) * args.ps,
velocity=args.ps / q.s,
pixel_size=args.ps)
# Move along y axis
traj_y = Trajectory(zip(y, x, z) * args.ps,
velocity=args.ps / q.s,
pixel_size=args.ps)
# Move along both x and y axes
traj_xy = Trajectory(zip(x, x, z) * args.ps,
velocity=args.ps / q.s,
pixel_size=args.ps)
# Circular trajectory of the composite body rotates around the image center and with radius
# n / 4 pixels.
circle = args.n / 2 * args.ps + make_circle(
).magnitude * args.n / 4 * args.ps
traj_circle = Trajectory(circle,
velocity=args.ps / q.s,
pixel_size=args.ps)
# Make the trajectory of the circle the same duration as the simple linear one.
traj_circle = Trajectory(circle,
velocity=traj_circle.length / traj_xy.length *
args.ps / q.s)
# three cubes in the same height and depth, shifted only along the x axis.
traj_stationary = Trajectory([(0, 0, 0)] * args.ps)
traj_stationary_1 = Trajectory([(-2 * edge, 0, 0)] * args.ps)
traj_stationary_2 = Trajectory([(2 * edge, 0, 0)] * args.ps)
cube = make_cube() / q.m * edge * args.ps
# The cubes are elongated along y axis.
cube[::2, :] /= 3
mesh = Mesh(cube, traj_x, orientation=geom.Y_AX)
mesh_2 = Mesh(cube, traj_y, orientation=geom.Y_AX)
mesh_3 = Mesh(cube, traj_xy, orientation=geom.Y_AX)
mesh_stationary = Mesh(cube, traj_stationary, orientation=geom.Y_AX)
mesh_stationary_1 = Mesh(cube, traj_stationary_1, orientation=geom.Y_AX)
mesh_stationary_2 = Mesh(cube, traj_stationary_2, orientation=geom.Y_AX)
bodies = [
mesh, mesh_2, mesh_3, mesh_stationary, mesh_stationary_1,
mesh_stationary_2
]
composite = CompositeBody(traj_circle,
bodies=bodies,
orientation=geom.Y_AX)
composite.bind_trajectory(args.ps)
total_time = composite.time
if args.t is None:
times = np.linspace(0, 1, 100)
else:
if args.t < 0 or args.t > 1:
raise ValueError('--t must be in the range [0, 1]')
times = [args.t]
im = None
for index, i in enumerate(times):
t = i * total_time
composite.clear_transformation()
composite.move(t)
p = composite.project(args.shape, args.ps).get()
if im is None:
im = show(p, title='Projection')
else:
im.set_data(p)
plt.draw()
plt.show()
def setUp(self):
syris.init(device_index=0)
self.triangles = make_cube()
self.trajectory = Trajectory([(0, 0, 0)] * q.m)
self.mesh = Mesh(self.triangles, self.trajectory)
