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 process(args, device_index):
import syris
from syris.geometry import Trajectory
from syris.bodies.mesh import Mesh, read_blender_obj
syris.init(device_index=device_index,
logfile=args.logfile,
double_precision=args.double_precision)
path, ext = os.path.splitext(args.input)
if ext == ".obj":
tri = read_blender_obj(args.input)
else:
tri = np.load(args.input)
tri = tri * q.um
tr = Trajectory([(0, 0, 0)] * q.um)
mesh = Mesh(tri, tr, center=None, iterations=args.supersampling_projection)
if args.n:
n = args.n
fov = n * args.pixel_size
else:
fov = max([ends[1] - ends[0] for ends in mesh.extrema[:-1]]) * 1.1
n = int(np.ceil((fov / args.pixel_size).simplified.magnitude))
shape = (n, n)
if args.make_gt:
LOG.info("--- Args info ---")
log_attributes(args)
return make_ground_truth(args, shape, mesh)
else:
num_projs = int(
np.pi *
n) if args.num_projections is None else args.num_projections
angles = np.linspace(0, args.rotation_angle, num_projs,
endpoint=False) * q.deg
if device_index == 0:
LOG.info("n: {}, ps: {}, FOV: {}".format(n, args.pixel_size, fov))
LOG.info("Total rotation angle: {} deg".format(
args.rotation_angle))
LOG.info("Number of projections: {}".format(num_projs))
LOG.info("--- Mesh info ---")
log_attributes(mesh)
LOG.info("--- Args info ---")
log_attributes(args)
return scan(
shape,
args.pixel_size,
args.rotation_axis,
mesh,
angles,
args.prefix,
lamino_angle=args.lamino_angle,
index=device_index,
num_devices=args.num_devices,
ss=args.supersampling,
)
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 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 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 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 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()
class TestMesh(SyrisTest):
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 shift_mesh(self, point):
triangles = self.triangles + np.array(point)[:,
np.newaxis] * point.units
return Mesh(triangles, self.trajectory, center=None)
def test_furthest_point(self):
self.assertAlmostEqual(get_magnitude(self.mesh.furthest_point),
np.sqrt(3))
def test_bounding_box(self):
bbox_points = get_magnitude(self.mesh.bounding_box.points).astype(
np.int).tolist()
seed = (-1, 1)
for point in itertools.product(seed, seed, seed):
self.assertTrue(list(point) in bbox_points)
def test_num_triangles(self):
self.assertEqual(12, self.mesh.num_triangles)
def test_extrema(self):
for endpoints in self.mesh.extrema:
self.assertAlmostEqual(-1, get_magnitude(endpoints[0]))
self.assertAlmostEqual(1, get_magnitude(endpoints[1]))
def test_center_of_gravity(self):
gt = (1, 2, 3) * q.m
mesh = self.shift_mesh(gt)
center = get_magnitude(mesh.center_of_gravity)
np.testing.assert_almost_equal(get_magnitude(gt), center)
def test_center_of_bbox(self):
gt = (1, 2, 3) * q.m
mesh = self.shift_mesh(gt)
center = get_magnitude(mesh.center_of_bbox)
np.testing.assert_almost_equal(get_magnitude(gt), center)
def test_diff(self):
gt = np.ones((3, 2)) * 2
np.testing.assert_almost_equal(gt, get_magnitude(self.mesh.diff))
def test_vectors(self):
ba, ca = self.mesh.vectors
a = self.triangles[:, ::3]
b = self.triangles[:, 1::3]
c = self.triangles[:, 2::3]
ba_gt = (b - a).transpose()
ca_gt = (c - a).transpose()
np.testing.assert_almost_equal(ba_gt, ba)
np.testing.assert_almost_equal(ca_gt, ca)
def test_areas(self):
np.testing.assert_almost_equal(2 * q.m**2, self.mesh.areas)
def test_normals(self):
v_0, v_1 = self.mesh.vectors
gt = np.cross(v_0, v_1) * q.um
np.testing.assert_almost_equal(gt, self.mesh.normals)
def test_max_triangle_x_diff(self):
self.assertEqual(2 * q.m, self.mesh.max_triangle_x_diff)
def test_sort(self):
self.mesh.sort()
x = get_magnitude(self.mesh.triangles[0, 2::3])
# Triangles must be sorted by the last vertex
np.testing.assert_almost_equal(x, sorted(x))
# The greatest is the last vertex in a triangle, all other vertices must be smaller
x = get_magnitude(self.mesh.triangles[0, :])
for i in range(0, len(x), 3):
self.assertTrue(x[i] <= x[i + 2])
self.assertTrue(x[i + 1] <= x[i + 2])
def test_get_degenerate_triangles(self):
triangles = get_magnitude(self.mesh.get_degenerate_triangles())
for i in range(0, triangles.shape[1], 3):
vertices = triangles[:, i:i + 3]
x = vertices[0, :]
y = vertices[1, :]
x_any = np.any(x - x[0])
y_any = np.any(y - y[0])
self.assertTrue(not (x_any and y_any))
self.mesh.rotate(45 * q.deg, X_AX)
self.mesh.rotate(45 * q.deg, Y_AX)
self.mesh.transform()
self.assertEqual(0, self.mesh.get_degenerate_triangles().shape[1])
def shift_mesh(self, point):
triangles = self.triangles + np.array(point)[:,
np.newaxis] * point.units
return Mesh(triangles, self.trajectory, center=None)
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)
class TestMesh(SyrisTest):
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 shift_mesh(self, point):
triangles = self.triangles + np.array(point)[:, np.newaxis] * point.units
return Mesh(triangles, self.trajectory, center=None)
def test_furthest_point(self):
self.assertAlmostEqual(get_magnitude(self.mesh.furthest_point), np.sqrt(3))
def test_bounding_box(self):
bbox_points = get_magnitude(self.mesh.bounding_box.points).astype(np.int).tolist()
seed = (-1, 1)
for point in itertools.product(seed, seed, seed):
self.assertTrue(list(point) in bbox_points)
def test_num_triangles(self):
self.assertEqual(12, self.mesh.num_triangles)
def test_extrema(self):
for endpoints in self.mesh.extrema:
self.assertAlmostEqual(-1, get_magnitude(endpoints[0]))
self.assertAlmostEqual(1, get_magnitude(endpoints[1]))
def test_center_of_gravity(self):
gt = (1, 2, 3) * q.m
mesh = self.shift_mesh(gt)
center = get_magnitude(mesh.center_of_gravity)
np.testing.assert_almost_equal(get_magnitude(gt), center)
def test_center_of_bbox(self):
gt = (1, 2, 3) * q.m
mesh = self.shift_mesh(gt)
center = get_magnitude(mesh.center_of_bbox)
np.testing.assert_almost_equal(get_magnitude(gt), center)
def test_diff(self):
gt = np.ones((3, 2)) * 2
np.testing.assert_almost_equal(gt, get_magnitude(self.mesh.diff))
def test_vectors(self):
ba, ca = self.mesh.vectors
a = self.triangles[:, ::3]
b = self.triangles[:, 1::3]
c = self.triangles[:, 2::3]
ba_gt = (b - a).transpose()
ca_gt = (c - a).transpose()
np.testing.assert_almost_equal(ba_gt, ba)
np.testing.assert_almost_equal(ca_gt, ca)
def test_areas(self):
np.testing.assert_almost_equal(2 * q.m ** 2, self.mesh.areas)
def test_normals(self):
v_0, v_1 = self.mesh.vectors
gt = np.cross(v_0, v_1) * q.um
np.testing.assert_almost_equal(gt, self.mesh.normals)
def test_max_triangle_x_diff(self):
self.assertEqual(2 * q.m, self.mesh.max_triangle_x_diff)
def test_sort(self):
self.mesh.sort()
x = get_magnitude(self.mesh.triangles[0, 2::3])
# Triangles must be sorted by the last vertex
np.testing.assert_almost_equal(x, sorted(x))
# The greatest is the last vertex in a triangle, all other vertices must be smaller
x = get_magnitude(self.mesh.triangles[0, :])
for i in range(0, len(x), 3):
self.assertTrue(x[i] <= x[i + 2])
self.assertTrue(x[i + 1] <= x[i + 2])
def test_get_degenerate_triangles(self):
triangles = get_magnitude(self.mesh.get_degenerate_triangles())
for i in range(0, triangles.shape[1], 3):
vertices = triangles[:, i:i + 3]
x = vertices[0, :]
y = vertices[1, :]
x_any = np.any(x - x[0])
y_any = np.any(y - y[0])
self.assertTrue(not (x_any and y_any))
self.mesh.rotate(45 * q.deg, X_AX)
self.mesh.rotate(45 * q.deg, Y_AX)
self.mesh.transform()
self.assertEqual(0, self.mesh.get_degenerate_triangles().shape[1])
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)
def read_collada(filename, scene_origin, orientation=geom.X_AX, mapping='xxyzz-y', iterations=1):
"""Read collada (*.dae) scene file *filename* and return list with objects of type Mesh. Place
it at *scene_origin*. *orientation* specifies the direction of orientation vectors for all
meshes. Scene objects must have materials assigned. For assigned material 'Material', a syris
material file 'Material.mat' is expected *filename*'s path. *mapping* can be used to change the
mapping of coordinate systems between syris and collada scenes. Standard is 'xxyzz-y' to make
z (collada) point upwards in syris (-y). Options are 'xxyyzz' and 'xxyzz-y'. *iterations* is
passed to all mesh objects.
Only geometry is imported, i.e there is currently no support for animated objects."""
e = xml.etree.ElementTree.parse(filename).getroot()
ns = {'co': 'http://www.collada.org/2005/11/COLLADASchema'}
scene_units = float(e.findall('co:asset/co:unit', ns)[0].get("meter")) * q.m
geometries = e.findall('co:library_geometries/co:geometry', ns)
visual_scene = e.find('co:library_visual_scenes/co:visual_scene', ns)
#animations = e.find('cp:library_animations/co:animation')
Meshes = []
for g in geometries:
geom_name = g.get("id")[:-5]
m = g.find('co:mesh', ns)
arrays = m.findall("co:source/co:float_array",ns)
pattern = re.compile(r'(?P<x>[0-9e.-]*) (?P<y>[0-9e.-]*) (?P<z>[0-9e.-]*) ')
vstr = arrays[0].text + " "
vertices = np.array(re.findall(pattern, vstr)).astype(np.float32)
polylistr = m.find('co:polylist/co:p', ns).text + " "
faces = np.array(polylistr.split()[::2]).astype(np.int)
triangles = vertices[faces]
if(mapping == 'xxyzz-y'):
# mapping corresponds to rotation around x-axis by 90 deg.
mat_mapping = geom.rotate(90* q.deg, geom.X_AX)
elif(mapping == 'xxyyzz'):
mat_mapping = np.identity(4)
else:
raise ValueError('Invalid mapping option for collada import.')
# above vertices are stored with respect to their object origin,
# transform them to obtain global vertex coordinates
# there are two possible ways to specify transformations in collada, matrix and transloc:
# find out which one was used and apply transformations
arg = "co:node[@name='" + geom_name + "']"
trafos = visual_scene.find(arg,ns)
if(trafos.find("co:rotate[@sid='rotationZ']", ns) is not None):
# TransLoc format
rotZ = float(trafos.find("co:rotate[@sid='rotationZ']", ns).text.split()[-1])
rotY = float(trafos.find("co:rotate[@sid='rotationY']", ns).text.split()[-1])
rotX = float(trafos.find("co:rotate[@sid='rotationX']", ns).text.split()[-1])
scale = map(float, trafos.find("co:scale[@sid='scale']", ns).text.split())
str_origin = trafos.find("co:translate[@sid='location']", ns).text.split()
origin = map(float, str_origin) * q.dimensionless
matr_x = geom.rotate(rotX * q.deg, geom.X_AX)
matr_y = geom.rotate(rotY * q.deg, geom.Y_AX)
matr_z = geom.rotate(rotZ * q.deg, geom.Z_AX)
mat_trans = geom.translate(origin)
mat_scale = geom.scale(scale)
# build transformation matrix
mat = np.dot(mat_mapping, mat_trans)
mat = np.dot(mat, mat_scale)
mat = np.dot(mat, matr_z)
mat = np.dot(mat, matr_y)
mat = np.dot(mat, matr_x)
elif (trafos.find("co:matrix[@sid='transform']", ns) is not None):
# Matrix format
str_mat = trafos.find("co:matrix[@sid='transform']", ns).text.split()
mat = np.dot(mat_mapping, np.array(str_mat, dtype = float).reshape(4,4))
else:
raise RuntimeError("Transformation type in collada file could not be determined.")
# apply transformation to vertices
for i, vert in enumerate(triangles):
vert = (tuple(vert) + (1,))
triangles[i] = np.dot(mat, vert)[:-1]
triangles = triangles.transpose()
# handle materials
material = m.find('co:polylist', ns).get("material")[:-9] + ".mat"
matname = os.path.join(os.path.dirname(filename), material)
if(not os.path.isfile(matname)):
raise RuntimeError("Materialfile {} not found. Files have to be in the same "\
"directory as the corresponding collada scene file.".format(matname))
m = make_fromfile(matname)
# create and add Mesh object
tr = geom.Trajectory(scene_origin)
mesh = Mesh(triangles * scene_units , tr, material = m, center = None,
orientation = orientation, iterations = iterations)
Meshes.extend([ mesh ])
return Meshes