def setUp(self):
default_syris_init()
lens = Lens(3.0, f_number=1.4, focal_length=100.0 * q.mm)
camera = Camera(1 * q.um, 0.1, 10, 1.0, 12, (64, 64))
detector = Detector(None, lens, camera)
ps = detector.pixel_size
t = np.linspace(0, 1, 10) * q.mm
x = t
y = np.zeros(len(t))
z = np.zeros(len(t))
points = list(zip(x, y, z)) * q.mm
mb_0 = MetaBall(
Trajectory(points,
pixel_size=ps,
furthest_point=1 * q.um,
velocity=1 * q.mm / q.s),
1 * q.um,
)
mb_1 = MetaBall(
Trajectory(points,
pixel_size=ps,
furthest_point=1 * q.um,
velocity=2 * q.mm / q.s),
1 * q.um,
)
self.experiment = Experiment([mb_0, mb_1], None, detector, 0 * q.m,
None)
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 test_composite_furthest_point(self):
mb_0 = MetaBall(Trajectory([(0, 0, 0)] * q.m), 1 * q.m)
mb_1 = MetaBall(Trajectory([(0, 0, 0)] * q.m), 2 * q.m)
composite = CompositeBody(Trajectory([(0, 0, 0)] * q.m), bodies=[mb_0, mb_1])
# Metaball's furthest point is twice the radius
self.assertAlmostEqual(4 * q.m, composite.furthest_point)
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_composite_bounding_box(self):
mb_0 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 0.5 * q.mm)
mb_1 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 1.5 * q.mm)
composite = CompositeBody(Trajectory([(0, 0, 0)] * q.mm, ),
bodies=[mb_0, mb_1])
transformed_0 = self._get_moved_bounding_box(mb_0, 90 * q.deg)
transformed_1 = self._get_moved_bounding_box(mb_1, -90 * q.deg)
def get_concatenated(t_0, t_1, index):
return np.concatenate((zip(*t_0)[index], zip(*t_1)[index])) * \
t_0[0].units
x_points = get_concatenated(transformed_0, transformed_1, 0)
y_points = get_concatenated(transformed_0, transformed_1, 1)
z_points = get_concatenated(transformed_0, transformed_1, 2)
x_min_max = min(x_points), max(x_points)
y_min_max = min(y_points), max(y_points)
z_min_max = min(z_points), max(z_points)
ground_truth = np.array(
list(itertools.product(x_min_max, y_min_max, z_min_max))) * q.m
np.testing.assert_almost_equal(ground_truth,
composite.bounding_box.points)
def setUp(self):
syris.init(device_index=0)
self.pixel_size = 1 * q.um
control_points = get_linear_points(geom.X, start=(1, 1, 1))
traj = Trajectory(control_points, velocity=1 * q.mm / q.s)
self.metaball = MetaBall(traj, 1 * q.mm)
self.metaball_2 = MetaBall(Trajectory(get_linear_points(geom.Z)), 2 * q.mm)
self.composite = CompositeBody(traj, bodies=[self.metaball, self.metaball_2])
def _run_parallel_or_opposite(self, sgn, gt):
n = 64
ps = 1 * q.um
y = np.linspace(0, sgn * n, num=10)
x = z = np.zeros(y.shape)
traj = Trajectory(zip(x, y, z) * ps, velocity=ps / q.s, pixel_size=ps)
mb = MetaBall(traj, n * ps / 16, orientation=geom.Y_AX)
mb.move(0 * q.s)
np.testing.assert_almost_equal(gt, mb.transform_matrix)
def create_metaballs(params, pixel_size):
x, y, z, r = list(zip(*params))
objects = b""
metaballs = []
for i in range(len(params)):
c_points = [(x[i], y[i], z[i])] * q.um
trajectory = Trajectory(c_points, pixel_size=pixel_size)
metaball = MetaBall(trajectory, r[i] * q.um)
metaball.move(0 * q.s)
metaballs.append(metaball)
objects += metaball.pack()
return metaballs, objects
def create_metaballs(params):
x, y, z, r = zip(*params)
objects = ""
metaballs = []
for i in range(len(params)):
c_points = [(x[i], y[i], z[i])] * q.um
trajectory = Trajectory(c_points)
metaball = MetaBall(trajectory, r[i] * q.um)
metaball.move(0 * q.s)
metaballs.append(metaball)
objects += metaball.pack()
return metaballs, objects
def test_get_distance(self):
n = 100
ps = 100 * q.mm
p = np.linspace(0, np.pi, n)
sin = np.sin(p)
cos = np.cos(p)
zeros = np.zeros(n)
# Simple body
# -----------
traj = Trajectory(zip(cos, sin, zeros) * q.m, velocity=1 * q.m / q.s)
ball = MetaBall(traj, .5 * q.m)
ball.bind_trajectory(ps)
dist = ball.get_distance(0 * q.s, ball.trajectory.time)
# Maximum along the x axis where the body travels 2 m by translation and rotates by 180
# degrees compared to position at t0, so the rotational displacement is 2 * furthest point,
# in this case 2 m, so altogether 4 m
self.assertAlmostEqual(dist.simplified.magnitude, 4)
# Composite body
# --------------
traj_m = Trajectory([(0, 0, 0)] * q.m)
ball = MetaBall(traj_m, .5 * q.m)
comp = CompositeBody(traj, bodies=[ball])
comp.bind_trajectory(ps)
d = comp.get_distance(0 * q.s, comp.time).simplified.magnitude
# 2 by translation and 180 degrees means 2 * furthest
gt = 2 * ball.furthest_point.simplified.magnitude + 2
self.assertAlmostEqual(gt, d, places=4)
d = comp.get_distance(0 * q.s, comp.time / 2).simplified.magnitude
# 1 by translation by either x or y and sqrt(2) * furthest by rotation
gt = 1 + comp.furthest_point.simplified.magnitude * np.sqrt(2)
self.assertAlmostEqual(gt, d, places=4)
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 test_composite_subbodies(self):
m_1 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 1 * q.mm)
m_2 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 2 * q.mm)
m_3 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 3 * q.mm)
m_4 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 4 * q.mm)
m_5 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 5 * q.mm)
m_6 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 6 * q.mm)
m_7 = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 7 * q.mm)
c_1 = CompositeBody(Trajectory([(0, 0, 0)] * q.mm),
bodies=[m_1, m_2])
c_2 = CompositeBody(Trajectory([(0, 0, 0)] * q.mm),
bodies=[m_3])
c_3 = CompositeBody(Trajectory([(0, 0, 0)] * q.mm),
bodies=[c_1, c_2])
c_4 = CompositeBody(Trajectory([(0, 0, 0)] * q.mm),
bodies=[m_4, m_5])
c_5 = CompositeBody(Trajectory([(0, 0, 0)] * q.mm),
bodies=[c_3, c_4, m_6, m_7])
# Empty composit body
CompositeBody(Trajectory([(0, 0, 0)] * q.mm))
# Empty composite body.
c_empty = CompositeBody(Trajectory([(0, 0, 0)] * q.mm))
self.assertEqual(c_empty.direct_primitive_bodies, [])
# Test direct subbodies
self.assertEqual(c_5.direct_primitive_bodies, [m_6, m_7])
self.assertEqual(c_3.direct_primitive_bodies, [])
# Add self.
with self.assertRaises(ValueError) as ctx:
c_5.add(c_5)
self.assertEqual("Cannot add self", ctx.exception.message)
# Add already contained primitive body.
with self.assertRaises(ValueError) as ctx:
c_5.add(m_1)
self.assertTrue(ctx.exception.message.endswith("already contained"))
# Add already contained composite body.
with self.assertRaises(ValueError) as ctx:
c_5.add(c_2)
self.assertTrue(ctx.exception.message.endswith("already contained"))
# Test all subbodies.
self.assertEqual(set(c_3.all_bodies),
set([m_1, m_2, m_3, c_1, c_2, c_3]))
self.assertEqual(set(c_1.all_bodies), set([c_1, m_1, m_2]))
self.assertEqual(c_empty.all_bodies, (c_empty,))
def _make_metaballs(args):
metaballs = []
radius = args.n / 16.
shift = 3 * radius
for i in range(-1, 2):
dx = i * 3 * radius
for j in range(-1, 2):
index = (i + 1) * 3 + (j + 1)
# Scale the metaballs to be [0.5, 1.0] radius large.
coeff = 0.5 + 0.5 / 8 * index
current_radius = coeff * radius
dy = j * 3 * radius
traj = Trajectory([(shift + dx, shift + dy, 0)] * args.ps,
pixel_size=args.ps)
metaballs.append(MetaBall(traj, current_radius * args.ps))
return metaballs
def create_sample(n, ps, radius=None, velocity=None, x_ends=None, y_ends=None):
"""Crete a metaball with a sine trajectory."""
fov = n * ps
if radius is None:
radius = n / 16 * ps
if x_ends is None:
radius_m = radius.simplified.magnitude
fov_m = fov.simplified.magnitude
x_ends = (radius_m, fov_m - radius_m) * q.m
if y_ends is None:
y_ends = (n / 4, 3 * n / 4) * ps
cp = make_sine(n=32, x_ends=x_ends, y_ends=y_ends)
if velocity is None:
velocity = 1 * q.mm / q.s
tr = Trajectory(cp, velocity=velocity)
mb = MetaBall(tr, radius)
return mb
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_metaball_bounding_box(self):
"""Bounding box moves along with its body."""
mb = MetaBall(Trajectory([(0, 0, 0)] * q.mm), 0.5 * q.mm)
transformed = self._get_moved_bounding_box(mb, 90 * q.deg)
np.testing.assert_almost_equal(transformed, mb.bounding_box.points)
