def test_make_1():
coords = np.array([[0, 0], [1, 0], [1, 1], [0, 1.]])
mesh = make_line_mesh(coords, close_path=True)
assert np.linalg.norm(mesh.coordinates() - coords) < 1E-13
cells = np.array([[0, 1], [1, 2], [2, 3], [0, 3]])
assert np.linalg.norm(mesh.cells() - cells) < 1E-13, mesh.cells()
def stitch(mesh, edges):
'''Remove edge and stitch together vertices'''
assert mesh.topology().dim() == 1
vertices = list(range(mesh.num_vertices()))
# We want to rewrite this such that given edges are
# kept but based on their connectivity we perform stitches
# changing other cells
e2v = mesh.topology()(1, 0)
# NOTE: by saying that edge is to be removed we're saying that its
# vertices can be regarded as same. A piece of graph of connected
# edges is thus a substitution rule that all vertices in that piece
# can be condensed
g = nx.Graph()
g.add_edges_from(map(e2v, edges))
rules = {}
# Substitution rule
for cc in sorted(nx.algorithms.connected_components(g), key=len):
substitute = cc.pop()
for node in cc:
assert node not in rules
rules[node] = substitute
# Edges are definitely part of the new mesh. Some other cells might
# be added as well if substitution produces two equal nodes
edges = list(edges)
# We want to keep a mapping from new mesh cell_idx to what was approx
# the parent cells in the oritinal mesh
cell_map, new_cells = [], []
# Now we rewrite
cells = mesh.cells().tolist()
for cell_id, cell in enumerate(cells):
if cell_id not in edges:
# Subs
if cell[0] in rules: cell[0] = rules[cell[0]]
if cell[1] in rules: cell[1] = rules[cell[1]]
# Invalid
cell[0] == cell[1] and edges.append(cell_id)
# A valid cell will keep it's position in new mesh
if cell[0] != cell[1]:
cell_map.append(cell_id)
new_cells.append(cell)
# Which vertices will be used; this is also a map from new to old
vertex_map = list(set(sum(new_cells, [])))
# Need to finally rewrte the cells this way; so vertex old -> new needed
ivertex_map = {o: n for n, o in enumerate(vertex_map)}
new_cells = np.fromiter((ivertex_map[v] for v in sum(new_cells, [])),
dtype='uintp').reshape((-1, 2))
new_coordinates = mesh.coordinates()[vertex_map]
return make_line_mesh(new_coordinates, new_cells), cell_map, vertex_map
def test_make_2():
coords = np.array([[0, 0, 2], [1, 0, 2], [1, 1, 2], [0, 1., 2]])
cells = np.array([[0, 1], [1, 2], [2, 3], [3, 0], [0, 2]])
mesh = make_line_mesh(coords, cells=cells)
assert np.linalg.norm(mesh.coordinates() - coords) < 1E-13
cells = np.array([[0, 1], [1, 2], [2, 3], [0, 3], [0, 2]])
cells0 = np.array(map(sorted, mesh.cells()))
assert np.linalg.norm(cells0 - cells) < 1E-13, mesh.cells()
assert mesh.ufl_cell() == ufl.Cell('interval', 3)
def refine(mesh, threshold):
'''Refine such that the new mesh has cell size of at most dx'''
assert mesh.topology().dim() == 1
e2v = mesh.topology()(1, 0)
cells = {old: [c.tolist()] for old, c in enumerate(mesh.cells())}
x = mesh.coordinates()
lengths = edge_lengths(mesh)
needs_refine = find_edges(lengths, predicate=lambda v, x: v > threshold)
next_v = len(x)
for cell in needs_refine:
v0, v1 = cells[cell].pop()
x0, x1 = x[v0], x[v1]
l = np.linalg.norm(x0 - x1)
nodes = [v0]
ts = np.linspace(0., 1., int(ceil(l / threshold)) + 1)[1:-1]
dx = x1 - x0
for t in ts:
xmid = x0 + t * dx
x = np.row_stack([x, xmid])
nodes.append(next_v)
next_v += 1
nodes.append(v1)
cells[cell] = list(zip(nodes[:-1], nodes[1:]))
# Mapping for
parent_cell_map = sum(([k] * len(cells[k]) for k in sorted(cells)), [])
cells = np.array(sum((cells[k] for k in sorted(cells)), []), dtype='uintp')
mesh = make_line_mesh(x, cells)
return mesh, np.array(parent_cell_map, dtype='uintp')
def curve_distance(edge_f, nlayers=4, outside_val=-1):
'''
Compute distance (P1) function that has for each vertex distance
from curve edge_f == 1.
'''
# Want to build a P1 function
mesh = edge_f.mesh()
V = df.FunctionSpace(mesh, 'CG', 1)
d = df.Function(V)
d_values = d.vector().get_local()
# Default
d_values[:] = outside_val
# Want to set points layer by layer
v2d = df.vertex_to_dof_map(V)
layers = layer_neighbor_vertex_generator(edge_f, nlayers=nlayers + 1)
curve_points = next(layers)
# On curve is 0
d_values[v2d[list(curve_points)]] = 0.
x = mesh.coordinates()
# For others we need to compute distance from edges
mesh.init(1, 0)
e2v = mesh.topology()(1, 0)
segments = np.row_stack(map(e2v, np.where(edge_f.array() == 1)[0]))
# In local numbering
vtx_idx, segments = np.unique(segments.flatten(), return_inverse=True)
line_mesh = make_line_mesh(x[vtx_idx], segments.reshape((-1, 2)))
tree = line_mesh.bounding_box_tree()
for points in map(list, layers):
d_values[v2d[points]] = np.fromiter(
(tree.compute_closest_entity(df.Point(x[p]))[1] for p in points),
dtype=float)
d.vector().set_local(d_values)
return d
def test():
coords = np.array([[0, 0], [1, 0], [1, 0.2], [1, 0.5], [1, 0.7], [1, 1],
[0, 1.]])
mesh = make_line_mesh(coords, close_path=True)
rmesh, mapping = refine(mesh, threshold=0.6)
x = mesh.coordinates()
y = rmesh.coordinates()
assert np.linalg.norm(x - y[:len(x)]) < 1E-13
e2v, E2V = mesh.topology()(1, 0), rmesh.topology()(1, 0)
for c in range(mesh.num_cells()):
x0, x1 = x[e2v(c)]
e = x1 - x0
e = e / np.linalg.norm(e)
for C in np.where(mapping == c)[0]:
y0, y1 = y[E2V(C)]
E = y1 - y0
E = E / np.linalg.norm(E)
assert abs(1 - abs(np.dot(e, E))) < 1E-13
# Mapping for
parent_cell_map = sum(([k] * len(cells[k]) for k in sorted(cells)), [])
cells = np.array(sum((cells[k] for k in sorted(cells)), []), dtype='uintp')
mesh = make_line_mesh(x, cells)
return mesh, np.array(parent_cell_map, dtype='uintp')
# --------------------------------------------------------------------
if __name__ == '__main__':
coords = np.array([[0, 0], [1, 0], [1, 0.2], [1, 0.5], [1, 0.7], [1, 1],
[0, 1.]])
mesh = make_line_mesh(coords, close_path=True)
rmesh, mapping = refine(mesh, threshold=0.6)
x = mesh.coordinates()
y = rmesh.coordinates()
assert np.linalg.norm(x - y[:len(x)]) < 1E-13
e2v, E2V = mesh.topology()(1, 0), rmesh.topology()(1, 0)
for c in range(mesh.num_cells()):
x0, x1 = x[e2v(c)]
e = x1 - x0
e = e / np.linalg.norm(e)
for C in np.where(mapping == c)[0]:
y0, y1 = y[E2V(C)]
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')