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Tools for matching topological entities (#1117)
* Add Mesh.p2f, Mesh.p2e, Mesh.p2t * use p2f to match boundaries in from_meshio * optimize also loading of oriented boundaries
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‎README.md

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@@ -212,8 +212,11 @@ with respect to documented and/or tested features.
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### Unreleased
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- Fixed: Tests now pass with `numpy==2.0rc1`
215-
- Fixed: `MappingAffine` uses lazy evaluation also for element mappings
216-
- Fixed: `MeshTet.init_tensor` uses less memory for large meshes
215+
- Fixed: `MappingAffine` now uses lazy evaluation also for element
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mappings, in addition to boundary mappings
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- Fixed: `MeshTet.init_tensor` uses significantly less memory for
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large meshes
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- Fixed: `Mesh.load` uses less memory when loading and matching tags
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- Added: `Basis` has new optional `disable_doflocs` kwarg which
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can be set to `True` to avoid computing `Basis.doflocs`, to reduce memory
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usage

‎docs/examples/meshes/tagged_gmsh4.msh

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$MeshFormat
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$PhysicalNames
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$EndElements

‎skfem/io/meshio.py

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@@ -1,5 +1,6 @@
11
"""Import/export any formats supported by meshio."""
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import logging
34
from pathlib import Path
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56
import meshio
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from skfem.generic_utils import OrientedBoundary
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14+
logger = logging.getLogger(__name__)
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1317
MESH_TYPE_MAPPING = {
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'tetra': MeshTet1,
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'tetra10': MeshTet2,
@@ -54,6 +58,9 @@ def from_meshio(m,
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ignore_orientation=False,
5559
ignore_interior_facets=False):
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61+
if ignore_interior_facets:
62+
logger.warning("kwarg ignore_interior_facets is unused.")
63+
5764
cells = m.cells_dict
5865
meshio_type = None
5966

@@ -121,56 +128,42 @@ def from_meshio(m,
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122129
# parse boundaries from cell_sets
123130
if m.cell_sets and bnd_type in m.cells_dict:
124-
oriented_facets = {
125-
k: [tuple(f) for f in m.cells_dict[bnd_type][v[bnd_type]]]
126-
for k, v in m.cell_sets_dict.items()
127-
if bnd_type in v and k.split(":")[0] != "gmsh"
128-
}
129-
sorted_facets = {k: [tuple(np.sort(f)) for f in v]
130-
for k, v in oriented_facets.items()}
131-
for k, v in oriented_facets.items():
132-
if ignore_orientation or ignore_interior_facets:
133-
a = np.array(sorted_facets[k])
134-
if ignore_interior_facets:
135-
b = mtmp.facets[:, mtmp.boundary_facets()].T
136-
else:
137-
b = mtmp.facets.T
138-
boundaries[k] = np.nonzero((a == b[:, None])
139-
.all(axis=2)
140-
.any(axis=1))[0]
141-
else:
142-
indices = []
143-
oris = []
144-
for i, f in enumerate(map(tuple, mtmp.facets.T)):
145-
if f in sorted_facets[k]:
146-
indices.append(i)
147-
ix = sorted_facets[k].index(f)
148-
facet = v[ix]
149-
t1, t2 = mtmp.f2t[:, i]
150-
if t2 == -1:
151-
# orientation on boundary is 0
152-
oris.append(0)
153-
continue
154-
if len(f) == 2:
155-
# rotate tangent to find normal
156-
tangent = (mtmp.p[:, facet[1]]
157-
- mtmp.p[:, facet[0]])
158-
normal = np.array([-tangent[1], tangent[0]])
159-
elif len(f) == 3:
160-
# cross product to find normal
161-
tangent1 = (mtmp.p[:, facet[1]]
162-
- mtmp.p[:, facet[0]])
163-
tangent2 = (mtmp.p[:, facet[2]]
164-
- mtmp.p[:, facet[0]])
165-
normal = -np.cross(tangent1, tangent2)
131+
p2f = mtmp.p2f
132+
for k, v in m.cell_sets_dict.items():
133+
if bnd_type in v and k.split(":")[0] != "gmsh":
134+
facets = m.cells_dict[bnd_type][v[bnd_type]].T
135+
sorted_facets = np.sort(facets, axis=0)
136+
ind = p2f[:, sorted_facets[0]]
137+
for itr in range(sorted_facets.shape[0] - 1):
138+
ind = ind.multiply(p2f[:, sorted_facets[itr + 1]])
139+
boundaries[k] = np.nonzero(ind)[0]
140+
141+
if not ignore_orientation:
142+
try:
143+
ori = np.zeros_like(boundaries[k], dtype=np.float64)
144+
t1, _ = mtmp.f2t[:, boundaries[k]]
145+
if facets.shape[0] == 2:
146+
tangents = (mtmp.p[:, facets[1]]
147+
- mtmp.p[:, facets[0]])
148+
normals = np.array([-tangents[1], tangents[0]])
149+
elif facets.shape[0] == 3:
150+
tangents1 = (mtmp.p[:, facets[1]]
151+
- mtmp.p[:, facets[0]])
152+
tangents2 = (mtmp.p[:, facets[2]]
153+
- mtmp.p[:, facets[0]])
154+
normals = -np.cross(tangents1.T, tangents2.T).T
166155
else:
167156
raise NotImplementedError
168-
# find another vector using node outside of boundary
169-
third = np.setdiff1d(mtmp.t[:, t1],
170-
np.array(f))[0]
171-
outplane = mtmp.p[:, f[0]] - mtmp.p[:, third]
172-
oris.append(1 if np.dot(normal, outplane) > 0 else 0)
173-
boundaries[k] = OrientedBoundary(indices, oris)
157+
for itr in range(mtmp.t.shape[0]):
158+
ori += np.sum(normals
159+
* (mtmp.p[:, facets[0]]
160+
- mtmp.p[:, mtmp.t[itr, t1]]),
161+
axis=0)
162+
ori = 1 * (ori > 0)
163+
boundaries[k] = OrientedBoundary(boundaries[k],
164+
ori)
165+
except Exception:
166+
logger.warning("Failure to orient a boundary.")
174167

175168
# MSH 2.2 tag parsing
176169
if len(boundaries) == 0 and m.cell_data and m.field_data:
@@ -212,7 +205,7 @@ def find_tagname(tag):
212205
boundaries[find_tagname(tag)] = index[tagindex, 1]
213206

214207
except Exception:
215-
pass
208+
logger.warning("Failure to parse tags from meshio.")
216209

217210
# attempt parsing skfem tags
218211
if m.cell_data:

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