def make_trajectory_sequence(args):
# Make a small circle (1 / 10 of the pixel size), so that the composite body only rotates and
# does not translate. Put this circle in the middle of the image.
circle = args.n / 2 * args.ps + make_circle(
n=1024).magnitude * args.ps / 10
traj = Trajectory(circle, velocity=args.ps / q.s, pixel_size=args.ps)
metaballs = _make_metaballs(args)
composite = CompositeBody(traj, bodies=metaballs)
im = None
d_angle = 10 * q.deg
fmt = 'Projection at rotation {:>9}'
# Rotate around 360 deg
for i, t in enumerate(
np.linspace(0, traj.time.simplified.magnitude, 37) * q.s):
# Reset transformation matrices
composite.clear_transformation()
# Move to the desired position, i.e. around the circle and then each metaball moves relative
# to the composite body.
composite.move(t)
p = composite.project(args.shape, args.ps).get()
if im is None:
im = show(p, title=fmt.format(i * d_angle))
else:
im.axes.set_title(fmt.format(i * d_angle))
im.set_data(p)
plt.draw()
plt.show()
def make_manual_sequence(args):
metaballs = _make_metaballs(args)
traj = Trajectory([(args.n / 2., args.n / 2., 0)] * args.ps,
pixel_size=args.ps)
composite = CompositeBody(traj, bodies=metaballs)
# Move the sub-bodies relative to the composite body and also move the composite body to the
# center of the image.
composite.move(0 * q.s)
im = None
d_angle = 10 * q.deg
fmt = 'Projection at rotation {:>9}'
# Rotate around 360 deg
for i in range(int((360 * q.deg / d_angle).magnitude) + 1):
p = composite.project(args.shape, args.ps).get()
if im is None:
im = show(p, title=fmt.format(i * d_angle))
else:
im.axes.set_title(fmt.format(i * d_angle))
im.set_data(p)
plt.draw()
# Rotation takes care of the relative rotation of the sub-bodies around the composite body.
composite.rotate(d_angle, geom.Z_AX)
plt.show()
def make_trajectory_sequence(args):
# Make a small circle (1 / 10 of the pixel size), so that the composite body only rotates and
# does not translate. Put this circle in the middle of the image.
circle = args.n / 2 * args.ps + make_circle(n=1024).magnitude * args.ps / 10
traj = Trajectory(circle, velocity=args.ps / q.s, pixel_size=args.ps)
metaballs = _make_metaballs(args)
composite = CompositeBody(traj, bodies=metaballs)
im = None
d_angle = 10 * q.deg
fmt = 'Projection at rotation {:>9}'
# Rotate around 360 deg
for i, t in enumerate(np.linspace(0, traj.time.simplified.magnitude, 37) * q.s):
# Reset transformation matrices
composite.clear_transformation()
# Move to the desired position, i.e. around the circle and then each metaball moves relative
# to the composite body.
composite.move(t)
p = composite.project(args.shape, args.ps).get()
if im is None:
im = show(p, title=fmt.format(i * d_angle))
else:
im.axes.set_title(fmt.format(i * d_angle))
im.set_data(p)
plt.draw()
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 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()
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_manual_sequence(args):
metaballs = _make_metaballs(args)
traj = Trajectory([(args.n / 2., args.n / 2., 0)] * args.ps, pixel_size=args.ps)
composite = CompositeBody(traj, bodies=metaballs)
# Move the sub-bodies relative to the composite body and also move the composite body to the
# center of the image.
composite.move(0 * q.s)
im = None
d_angle = 10 * q.deg
fmt = 'Projection at rotation {:>9}'
# Rotate around 360 deg
for i in range(int((360 * q.deg / d_angle).magnitude) + 1):
p = composite.project(args.shape, args.ps).get()
if im is None:
im = show(p, title=fmt.format(i * d_angle))
else:
im.axes.set_title(fmt.format(i * d_angle))
im.set_data(p)
plt.draw()
# Rotation takes care of the relative rotation of the sub-bodies around the composite body.
composite.rotate(d_angle, geom.Z_AX)
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()
