def test_get_next_time(self):
n = 100
ps = 100 * q.mm
psm = ps.simplified.magnitude
p = np.linspace(0, np.pi, n)
sin = np.sin(p) * 1e-3
cos = np.cos(p) * 1e-3
zeros = np.zeros(n)
traj_m_0 = Trajectory(zip(p * 1e-3, zeros, zeros) * q.m,
velocity=1 * q.mm / q.s)
traj_m_1 = Trajectory([(0, 0, 0)] * q.m)
ball_0 = MetaBall(traj_m_0, .5 * q.m)
ball_1 = MetaBall(traj_m_1, .5 * q.m)
traj = Trajectory(zip(cos, sin, zeros) * q.m, velocity=1 * q.mm / q.s)
comp = CompositeBody(traj, bodies=[ball_0, ball_1])
dt = comp.get_maximum_dt(ps)
# Normal trajectories
# Test the beginning, middle and end because of time complexity
for t_0 in [0 * q.s, comp.time / 2, comp.time - 10 * dt]:
t_1 = comp.get_next_time(t_0, ps)
d = comp.get_distance(t_0, t_1).simplified.magnitude
np.testing.assert_almost_equal(psm, d)
# Trajectories which sum up to no movement
traj_m = Trajectory(zip(zeros, -p, zeros) * q.m,
velocity=1 * q.mm / q.s)
ball = MetaBall(traj_m, .5 * q.m)
traj = Trajectory(zip(p, zeros, zeros) * q.m, velocity=1 * q.mm / q.s)
comp = CompositeBody(traj, bodies=[ball])
self.assertEqual(np.inf * q.s, comp.get_next_time(0 * q.s, ps))
def test_static_composite(self):
ps = 1 * q.um
traj = Trajectory([(0, 0, 0)] * q.m)
mb_0 = MetaBall(traj, 10 * q.um)
mb_1 = MetaBall(traj, 10 * q.um)
comp = CompositeBody(traj, bodies=[mb_0, mb_1])
self.assertEqual(np.inf * q.s, comp.get_next_time(0 * q.s, ps))
def main():
syris.init()
args = parse_args()
n = 256
shape = (n, n)
ps = 1 * q.um
num_projections = None
cube_edge = n / 4 * ps
fmt = os.path.join(args.output, "projection_{:04}.tif")
x = np.linspace(n // 4 + n // 8, 3 * n // 4 + n // 8, num=10)
y = z = np.zeros(x.shape)
cube_0 = make_cube_body(n, ps, cube_edge)
cube_1 = make_cube_body(n, ps, cube_edge, phase_shift=np.pi * q.rad)
# Vertical motion component has such velocity that the cubes are displaced by their edge length
# 1 pixel for making sure we have one "complete" sinogram
velocity = (cube_edge - ps) / cube_0.trajectory.time
traj_y = geom.Trajectory(list(zip(y, x, z)) * ps,
pixel_size=ps,
velocity=velocity)
composite = CompositeBody(traj_y, bodies=[cube_0, cube_1])
# Total time is the rotation time because we want one tomographic data set
total_time = cube_0.trajectory.time
dt = composite.get_next_time(0 * q.s, ps)
if num_projections is None:
num_projections = int(np.ceil((total_time / dt).simplified.magnitude))
print(" num_projs:", num_projections)
print(" rotation time:", cube_0.trajectory.time)
print(" vertical motion time:", traj_y.time)
print(" simulation time:", total_time)
for i in range(num_projections):
t = total_time / num_projections * i
composite.move(t)
projection = composite.project(shape, ps).get()
imageio.imwrite(fmt.format(i), projection)
show(projection)
plt.show()
def main():
syris.init()
args = parse_args()
n = 256
shape = (n, n)
ps = 1 * q.um
num_projections = None
cube_edge = n / 4 * ps
fmt = os.path.join(args.output, 'projection_{:04}.tif')
x = np.linspace(n / 4 + n / 8, 3 * n / 4 + n / 8, num=10)
y = z = np.zeros(x.shape)
cube_0 = make_cube_body(n, ps, cube_edge)
cube_1 = make_cube_body(n, ps, cube_edge, phase_shift=np.pi * q.rad)
# Vertical motion component has such velocity that the cubes are displaced by their edge length
# 1 pixel for making sure we have one "complete" sinogram
velocity = (cube_edge - ps) / cube_0.trajectory.time
traj_y = geom.Trajectory(zip(y, x, z) * ps, pixel_size=ps, velocity=velocity)
composite = CompositeBody(traj_y, bodies=[cube_0, cube_1])
# Total time is the rotation time because we want one tomographic data set
total_time = cube_0.trajectory.time
dt = composite.get_next_time(0 * q.s, ps)
if num_projections is None:
num_projections = int(np.ceil((total_time / dt).simplified.magnitude))
print ' num_projs:', num_projections
print ' rotation time:', cube_0.trajectory.time
print ' vertical motion time:', traj_y.time
print ' simulation time:', total_time
for i in range(num_projections):
t = total_time / num_projections * i
composite.move(t)
projection = composite.project(shape, ps).get()
tifffile.imsave(fmt.format(i), projection)
show(projection)
plt.show()
