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 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 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)