def test_point_skew_2d(niters=1, **kwargs):
'''Not necesarily conform'''
mesh1d = _1d2d_mesh(4)
embedding = embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_points',
gmsh_args=[],
niters=niters,
debug=False,
save_geo='',
**kwargs)
skewed = embedding.nc_edge_encoding.as_vertices
assert skewed
x = embedding.embedding_mesh.coordinates()
embedding.embedding_mesh.init(1, 0)
embedding.embedding_mesh.init(0, 1)
E2V, V2E = embedding.embedding_mesh.topology()(1, 0), embedding.embedding_mesh.topology()(0, 1)
compute_star = lambda v: set(np.hstack([E2V(ei) for ei in V2E(v)]))
y = mesh1d.coordinates()
e2v = mesh1d.topology()(1, 0)
for edge in skewed:
y0, y1 = y[e2v(edge)]
for piece in skewed[edge]:
if not len(piece) == 3:
continue
x0, x2, x1 = x[piece]
# End points were inserted correctly
assert is_on_line(x0, y0, y1)
v0, v2, v1 = piece
# Mid point is in the star
mids = compute_star(v0) & compute_star(v1)
assert v2 in mids
# If there are more this way we get a shortest path
if len(mids) > 1:
path_length = lambda v: np.linalg.norm(x[v0] - x[v], 2) + np.linalg.norm(x[v1] - x[v], 2)
assert v2 == min(mids, key=path_length)
vmap = embedding.vertex_map
encode = embedding.edge_encoding.as_edges
# We can combine the maps to pick correctly embedded edges
for edge in range(mesh1d.num_cells()):
if edge not in skewed:
v0, v1 = e2v(edge)
e_ = encode[edge]
print e_, '<--'
vs = set(vmap[e2v(e_[0])])
assert v0 not in vs
vs = set(vmap[e2v(e_[-1])])
assert v1 in vs
def test_line_2d():
'''Not skew'''
mesh1d = _1d2d_mesh(3)
embedding = embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_lines',
gmsh_args=[],
debug=False,
save_geo='')
# assert not status
assert _embed_vertex(mesh1d, embedding)
assert _embed_edgecolor(mesh1d, embedding)
assert _embed_edgeencode(mesh1d, embedding)
def test_point_stl_3d():
'''Not skew'''
mesh1d = _1d3d_mesh(3)
embedding = embed_mesh1d(mesh1d,
bounding_shape='box.stl',
how='as_points',
gmsh_args=[],
debug=False,
save_geo='')
# assert not status
assert _embed_vertex(mesh1d, embedding)
assert _embed_edgecolor(mesh1d, embedding)
assert _embed_edgeencode(mesh1d, embedding)
def test_line_3d():
'''Not skew'''
mesh1d = _1d3d_mesh(3)
embedding = embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_lines',
gmsh_args=[],
debug=False,
save_geo='')
f = df.MeshFunction('size_t', mesh1d, 1, 0)
f.array()[:] = np.random.randint(1, 5, f.size())
assert _edge_transfer(f, embedding)
def test_point_3d_vertex():
'''Not skew'''
mesh1d = _1d3d_mesh(3)
embedding = embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_points',
gmsh_args=[],
debug=False,
save_geo='')
f = df.MeshFunction('double', mesh1d, 0, 0)
f.array()[:] = mesh1d.coordinates()[:, 0]
assert _vertex_transfer(f, embedding)
def test_line_2d_vertex():
'''Not skew'''
mesh1d = _1d2d_mesh(3)
embedding = embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_lines',
gmsh_args=[],
debug=False,
save_geo='')
f = df.MeshFunction('double', mesh1d, 0, 0)
f.array()[:] = np.linalg.norm(mesh1d.coordinates(), np.inf, axis=1)
assert _vertex_transfer(f, embedding)
def test_point_skew_stl_3d():
'''Not necesarily conform'''
mesh1d = _1d3d_mesh(4)
embedding = embed_mesh1d(mesh1d,
bounding_shape='box.stl',
how='as_points',
gmsh_args=[],
niters=1,
debug=False,
save_geo='')
skewed = embedding.nc_edge_encoding.as_vertices
assert skewed
x = embedding.embedding_mesh.coordinates()
embedding.embedding_mesh.init(1, 0)
embedding.embedding_mesh.init(0, 1)
E2V, V2E = embedding.embedding_mesh.topology()(1, 0), embedding.embedding_mesh.topology()(0, 1)
compute_star = lambda v: set(np.hstack([E2V(ei) for ei in V2E(v)]))
y = mesh1d.coordinates()
e2v = mesh1d.topology()(1, 0)
for edge in skewed:
y0, y1 = y[e2v(edge)]
for piece in skewed[edge]:
assert len(piece) == 3
x0, x2, x1 = x[piece]
# End points were inserted correctly
assert is_on_line(x0, y0, y1)
v0, v2, v1 = piece
# Mid point is in the star
mids = compute_star(v0) & compute_star(v1)
assert v2 in mids
# If there are more this way we get a shortest path
if len(mids) > 1:
path_length = lambda v: np.linalg.norm(x[v0] - x[v], 2) + np.linalg.norm(x[v1] - x[v], 2)
assert v2 == min(mids, key=path_length)
def test_save():
'''Not necesarily conform'''
mesh1d = _1d3d_mesh(4)
embedding = embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_points',
gmsh_args=[],
niters=1,
debug=False,
save_geo='')
save_embedding(embedding, 'foo/bar')
paths = [
os.path.join('foo/bar', buz)
for buz in ('mesh.h5', 'vertex_map.txt', 'edge_encoding_0.pkl',
'edge_encoding_1.pkl', 'nc_edge_encoding_0.pkl',
'nc_edge_encoding_1.pkl')
]
assert all(map(os.path.exists, paths))
def test_load():
mesh1d = _1d3d_mesh(4)
embedding = embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_points',
gmsh_args=[],
niters=1,
debug=False,
save_geo='')
embedding0 = load_embedding(save_embedding(embedding, 'foo/bar'))
assert embedding.edge_encoding == embedding0.edge_encoding
assert embedding.nc_edge_encoding == embedding0.nc_edge_encoding
assert np.linalg.norm(embedding.vertex_map - embedding0.vertex_map) < 1E-13
assert np.linalg.norm(embedding.edge_coloring.array() -
embedding0.edge_coloring.array()) < 1E-13
assert np.linalg.norm(embedding.embedding_mesh.coordinates() -
embedding0.embedding_mesh.coordinates()) < 1E-13
assert np.linalg.norm(embedding.embedding_mesh.cells() -
embedding0.embedding_mesh.cells()) < 1E-13
df.File('original.pvd') << original_coloring
# Getting thick enough vessels
radius_filter = lambda v, x: v > 4.5
# 0) Just filter on radius
if True:
idx = find_edges(radius, predicate=radius_filter)
rmesh, rcmap, rlmap = make_submesh(mesh1d, idx)
df.File('meshr.pvd') << rmesh
embedding = embed_mesh1d(rmesh,
bounding_shape=0.01,
how='as_lines',
gmsh_args=list(sys.argv),
save_geo='model',
save_msh='model',
save_embedding='rat_timo')
# This is a check that mesh is okay for solving
edge_f = embedding.edge_coloring
df.File('rat_timo/embedded_r.pvd') << edge_f
edge_f.array()[edge_f.array() > 0] = 1
from perfusion.boundary_conditions import poisson_solve, EdgeDirichletBC
V = df.FunctionSpace(embedding.embedding_mesh, 'CG', 1)
f = df.Constant(1)
bcs = EdgeDirichletBC(V, 2, edge_f, 1)
from mbed.generation import make_line_mesh
from mbed.meshing import embed_mesh1d
import numpy as np
import sys
coords = np.array([[0, 0], [1, 0], [1, 1], [0, 1.]])
mesh1d = make_line_mesh(coords, close_path=True)
embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_lines',
gmsh_args=sys.argv,
save_geo='model',
save_msh='model',
save_embedding='test_embed_line')
print()
embed_mesh1d(mesh1d,
bounding_shape=0.1,
how='as_points',
gmsh_args=sys.argv,
save_geo='model',
save_msh='model',
niters=2,
save_embedding='test_embed_point')