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=nm.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=nm.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()