Source code for extract_edges
#!/usr/bin/env python
"""
Extract outline edges of a given mesh and save them into
'<original path>/edge_<original mesh file name>.vtk'
or into a user defined output file.
The outline edge is an edge for which norm(nvec1 - nvec2) < eps,
where nvec1 and nvec2 are the normal vectors of the incident facets.
"""
from __future__ import absolute_import
import numpy as nm
from scipy.sparse import coo_matrix
import sys
sys.path.append('.')
from argparse import ArgumentParser
from sfepy.base.base import output, Struct
from sfepy.base.ioutils import edit_filename
from sfepy.discrete.fem import Mesh, FEDomain
from sfepy.discrete.fem.meshio import MeshioLibIO
[docs]def merge_lines(mesh, eps=1e-18):
coors, ngroups, conns, mat_ids, ctype = mesh
conns = conns[0]
# vertices to edges map
n_v = coors.shape[0]
n_e = conns.shape[0]
row = nm.repeat(nm.arange(n_e), 2)
aux = coo_matrix((nm.ones((n_e * 2,), dtype=bool),
(row, conns.flatten())), shape=(n_e, n_v))
v2e = aux.tocsc()
n_epv = nm.diff(v2e.indptr)
# directional vectors of edges
de = coors[conns[:, 1], :] - coors[conns[:, 0], :]
de = de / nm.linalg.norm(de, axis=1)[:, nm.newaxis]
eflag = nm.ones((n_e, ), dtype=bool)
valid_e = nm.where(eflag)[0]
e_remove = []
while len(valid_e) > 0:
ie = valid_e[0]
d = de[ie]
buff = [(ie, conns[ie, 0]), (ie, conns[ie, 1])]
eflag[ie] = False # invalidate edge
while len(buff) > 0:
e, v = buff.pop(-1)
if n_epv[v] == 2:
idx = v2e.indptr[v]
aux = v2e.indices[idx]
next_e = v2e.indices[idx + 1] if aux == e else aux
if not eflag[next_e]: # valid edge?
continue
if nm.linalg.norm(de[next_e] - d) < eps\
or nm.linalg.norm(de[next_e] + d) < eps:
next_ec = conns[next_e, :]
new_v = next_ec[0] if next_ec[1] == v else next_ec[1]
idx = 0 if conns[e, 0] == v else 1
conns[e, idx] = new_v # reconnect edge
idx = v2e.indptr[new_v]
aux = v2e.indices[idx]
idx += 0 if aux == next_e else 1
v2e.indices[idx] = e # update v2e map
buff.append((e, new_v)) # continue in searching
eflag[next_e] = False # invalidate edge
e_remove.append(next_e)
valid_e = nm.where(eflag)[0]
if len(e_remove) > 0:
# remove unused edges and vertices
eflag.fill(True)
eflag[nm.asarray(e_remove)] = False
remap = -nm.ones((n_v, ), dtype=nm.int64)
remap[conns[eflag, :]] = 1
vidx = nm.where(remap > 0)[0]
remap[vidx] = nm.arange(len(vidx))
conns_new = remap[conns[eflag, :]]
return coors[vidx, :], ngroups[vidx],\
[conns_new], [mat_ids[0][eflag]], ctype
else:
return mesh
[docs]def extract_edges(mesh, eps=1e-16):
"""
Extract outline edges of a given mesh.
The outline edge is an edge for which norm(nvec_1 - nvec_2) < eps,
where nvec_1 and nvec_2 are the normal vectors of the incident facets.
Parameters
----------
mesh : Mesh
The 3D or 2D mesh.
eps : float
The tolerance parameter of the outline edge searching algorithm.
Returns
-------
mesh_out : tuple
The data of the outline mesh, Mesh.from_data() format, i.e.
(coors, ngroups, ed_conns, mat_ids, descs).
"""
domain = FEDomain('domain', mesh)
cmesh = domain.cmesh
output('Mesh - dimension: %d, vertices: %d, elements: %d'
% (mesh.dim, mesh.n_nod, mesh.n_el))
if mesh.dim == 2:
oedges = cmesh.get_surface_facets()
mesh_coors = nm.hstack([cmesh.coors,
nm.zeros((cmesh.coors.shape[0], 1))])
elif mesh.dim == 3:
cmesh.setup_connectivity(1, 2)
cmesh.setup_connectivity(3, 2)
sfaces = cmesh.get_surface_facets()
_, idxs = nm.unique(cmesh.get_conn(3, 2).indices, return_index=True)
normals = cmesh.get_facet_normals()[idxs, :]
se_map, se_off = cmesh.get_incident(1, sfaces, 2, ret_offsets=True)
sedges = nm.unique(se_map)
n_se = sedges.shape[0]
# remap surface edges to continuous range
se_remap = -nm.ones(sedges.max() + 1)
se_remap[sedges] = nm.arange(n_se)
se_map0 = se_remap[se_map]
# surface face/edge connectivity matrix (n_surf x n_edge)
n_ef = nm.diff(se_off)[0] # = 2
n_sf = se_map.shape[0] // n_ef
row = nm.repeat(nm.arange(n_sf), n_ef)
sf2e = coo_matrix((nm.ones((n_sf * n_ef,), dtype=bool),
(row , se_map0)), shape=(n_sf, n_se))
# edge to face map (n_edge x 2)
se2f = sf2e.tocsc().indices.reshape((sedges.shape[0], 2))
snormals = normals[sfaces]
err = nm.linalg.norm(snormals[se2f[:, 0]] - snormals[se2f[:, 1]],
axis=1)
oedges = sedges[nm.where(err > eps)[0]]
mesh_coors = cmesh.coors
else:
raise NotImplementedError
# save outline mesh
if oedges.shape[0] > 0:
ec_idxs = nm.unique(cmesh.get_incident(0, oedges, 1))
ed_coors = mesh_coors[ec_idxs, :]
ngroups = nm.zeros((ed_coors.shape[0],), dtype=nm.int16)
aux = cmesh.get_conn(1, 0).indices
ed_conns = aux.reshape((aux.shape[0] // 2, 2))[oedges, :]
ec_remap = -nm.ones((ec_idxs.max() + 1, ), dtype=nm.int64)
ec_remap[ec_idxs] = nm.arange(ec_idxs.shape[0])
ed_conns = ec_remap[ed_conns]
mat_ids = nm.ones((ed_conns.shape[0],), dtype=nm.int16)
mesh_out = ed_coors, ngroups, [ed_conns], [mat_ids], ['3_2']
return mesh_out
else:
raise ValueError('no outline edges found (eps=%e)!' % eps)
helps = {
'eps': 'tolerance parameter of the edge search algorithm (default: 1e-12)',
'filename-out': 'name of output file',
}
[docs]def main():
parser = ArgumentParser(description=__doc__)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('--eps', action='store', dest='eps',
default=1e-12, help=helps['eps'])
parser.add_argument('-o', '--filename-out',
action='store', dest='filename_out',
default=None, help=helps['filename-out'])
parser.add_argument('filename')
options = parser.parse_args()
filename = options.filename
mesh = Mesh.from_file(filename)
mesh_out = extract_edges(mesh, eps=float(options.eps))
mesh_out = merge_lines(mesh_out)
filename_out = options.filename_out
if filename_out is None:
filename_out = edit_filename(filename, prefix='edge_', new_ext='.vtk')
output('Outline mesh - vertices: %d, edges: %d, output filename: %s'
% (mesh_out[0].shape[0], mesh_out[2][0].shape[0], filename_out))
# hack to write '3_2' elements - edges
io = MeshioLibIO()
aux_mesh = Struct()
aux_mesh._get_io_data = lambda: mesh_out
aux_mesh.n_el = mesh_out[2][0].shape[0]
io.write(filename_out, aux_mesh)
if __name__ == '__main__':
main()