def test_npc_like(self):
"""Test that nested transforms match in IMP and RMF with npc-like config"""
coords = list(IMP.algebra.get_random_vector_in(
IMP.algebra.get_unit_sphere_3d()))
name = RMF._get_temporary_file_path("test_transform_npc.rmfz")
fh = RMF.create_rmf_file(name)
rr0 = IMP.algebra.get_random_rotation_3d()
t0 = IMP.algebra.get_random_vector_in(IMP.algebra.get_unit_sphere_3d())
rff = RMF.ReferenceFrameFactory(fh)
rfcf = RMF.ReferenceFrameFactory(fh)
pf = RMF.ParticleFactory(fh)
ch0 = fh.get_root_node().add_child("ch0", RMF.REPRESENTATION)
n0 = ch0.add_child("n0", RMF.REPRESENTATION)
n1 = ch0.add_child("n1", RMF.REPRESENTATION)
n2 = ch0.add_child("n2", RMF.REPRESENTATION)
rff.get(ch0).set_translation(RMF.Vector3(*t0))
rff.get(ch0).set_rotation(RMF.Vector4(*rr0.get_quaternion()))
pf.get(ch0).set_coordinates(RMF.Vector3(0, 0, 0))
pf.get(ch0).set_radius(1)
pf.get(ch0).set_mass(1)
pf.get(n0).set_coordinates(RMF.Vector3(1, 0, 0))
pf.get(n0).set_mass(1)
pf.get(n0).set_radius(1)
pf.get(n1).set_coordinates(RMF.Vector3(0, 1, 0))
pf.get(n1).set_mass(1)
pf.get(n1).set_radius(1)
pf.get(n2).set_coordinates(RMF.Vector3(0, 0, 1))
pf.get(n2).set_mass(1)
pf.get(n2).set_radius(1)
tr = IMP.algebra.Transformation3D(rr0, t0)
ctro = RMF.CoordinateTransformer()
ctr = RMF.CoordinateTransformer(ctro, rfcf.get(ch0))
vch0 = ctr.get_global_coordinates(pf.get(ch0).get_coordinates())
vn0 = ctr.get_global_coordinates(pf.get(n0).get_coordinates())
vn1 = ctr.get_global_coordinates(pf.get(n1).get_coordinates())
vn2 = ctr.get_global_coordinates(pf.get(n2).get_coordinates())
vich0 = tr.get_transformed(IMP.algebra.Vector3D(0, 0, 0))
vin0 = tr.get_transformed(IMP.algebra.Vector3D(1, 0, 0))
vin1 = tr.get_transformed(IMP.algebra.Vector3D(0, 1, 0))
vin2 = tr.get_transformed(IMP.algebra.Vector3D(0, 0, 1))
print IMP.algebra.get_distance(vin0, vich0),\
IMP.algebra.get_distance(vin1, vich0),\
IMP.algebra.get_distance(vin2, vich0)
for p in [(vch0, vich0), (vn0, vin0), (vn1, vin1), (vn2, vin2)]:
print p[0], p[1]
self.assertAlmostEqual(
IMP.algebra.get_distance(p[1],
IMP.algebra.Vector3D(*p[0])),
0,
delta=.1)
def visit(node, reference_frame, reference_frame_factory, particle_factory,
segment_factory, ball_factory):
if reference_frame_factory.get_is(node):
reference_frame = RMF.CoordinateTransformer(
reference_frame, reference_frame_factory.get(node))
print("reference frame is now", reference_frame)
elif segment_factory.get_is(node):
segment = segment_factory.get(node)
print("segment", node.get_name())
# silliness
coords = segment.get_coordinates()
for i in range(0, len(coords[0])):
print_coordinates(reference_frame,
[coords[0][i], coords[1][i], coords[2][i]])
elif particle_factory.get_is(node):
particle = particle_factory.get(node)
print("particle", node.get_name(),
print_coordinates(reference_frame, particle.get_coordinates()))
elif ball_factory.get_is(node):
particle = ball_factory.get(node)
print("ball", node.get_name(),
print_coordinates(reference_frame, particle.get_coordinates()))
for c in node.get_children():
visit(c, reference_frame, reference_frame_factory, particle_factory,
segment_factory, ball_factory)
def test_simple(self):
"""Test that nested transforms match in IMP and RMF"""
coords = list(IMP.algebra.get_random_vector_in(
IMP.algebra.get_unit_sphere_3d()))
name = RMF._get_temporary_file_path("test_transform.rmfz")
fh = RMF.create_rmf_file(name)
rr0 = IMP.algebra.get_random_rotation_3d()
rr1 = IMP.algebra.get_random_rotation_3d()
t0 = IMP.algebra.get_random_vector_in(IMP.algebra.get_unit_sphere_3d())
t1 = IMP.algebra.get_random_vector_in(IMP.algebra.get_unit_sphere_3d())
rff = RMF.ReferenceFrameFactory(fh)
rfcf = RMF.ReferenceFrameFactory(fh)
pf = RMF.ParticleFactory(fh)
ch0 = fh.get_root_node().add_child("ch0", RMF.REPRESENTATION)
ch1 = ch0.add_child("ch1", RMF.REPRESENTATION)
n = ch1.add_child("n", RMF.REPRESENTATION)
rff.get(ch0).set_translation(RMF.Vector3(*t0))
rff.get(ch1).set_translation(RMF.Vector3(*t1))
rff.get(ch0).set_rotation(RMF.Vector4(*rr0.get_quaternion()))
rff.get(ch1).set_rotation(RMF.Vector4(*rr1.get_quaternion()))
pf.get(n).set_coordinates(RMF.Vector3(*coords))
pf.get(n).set_radius(1)
pf.get(n).set_mass(1)
tr = IMP.algebra.Transformation3D(
rr0,
t0) * IMP.algebra.Transformation3D(
rr1,
t1)
ctro = RMF.CoordinateTransformer()
ctri = RMF.CoordinateTransformer(ctro, rfcf.get(ch0))
ctr = RMF.CoordinateTransformer(ctri, rfcf.get(ch1))
vr = ctr.get_global_coordinates(pf.get(n).get_coordinates())
vi = tr.get_transformed(IMP.algebra.Vector3D(*coords))
print vr, vi
self.assertAlmostEqual(
IMP.algebra.get_distance(vi,
IMP.algebra.Vector3D(*vr)),
0,
delta=.1)
if reference_frame_factory.get_is(node):
reference_frame = RMF.CoordinateTransformer(
reference_frame, reference_frame_factory.get(node))
print("reference frame is now", reference_frame)
elif segment_factory.get_is(node):
segment = segment_factory.get(node)
print("segment", node.get_name())
# silliness
coords = segment.get_coordinates()
for i in range(0, len(coords[0])):
print_coordinates(reference_frame,
[coords[0][i], coords[1][i], coords[2][i]])
elif particle_factory.get_is(node):
particle = particle_factory.get(node)
print("particle", node.get_name(),
print_coordinates(reference_frame, particle.get_coordinates()))
elif ball_factory.get_is(node):
particle = ball_factory.get(node)
print("ball", node.get_name(),
print_coordinates(reference_frame, particle.get_coordinates()))
for c in node.get_children():
visit(c, reference_frame, reference_frame_factory, particle_factory,
segment_factory, ball_factory)
fh = RMF.open_rmf_file_read_only(RMF.get_example_path("reference_frames.rmf3"))
visit(fh.get_root_node(), RMF.CoordinateTransformer(),
RMF.ReferenceFrameFactory(fh), RMF.ParticleFactory(fh),
RMF.SegmentFactory(fh), RMF.BallFactory(fh))
