Merge pull request #1234 from nschloe/cellblock-dim

add cell_block.dim, many gmsh fixes

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = meshio
-version = 5.1.0
+version = 5.1.1
 author = Nico Schlömer et al.
 author_email = [email protected]
 description = I/O for many mesh formats

src/meshio/__init__.py

@@ -32,7 +32,6 @@
     xdmf,
 )
 from .__about__ import __version__
-from ._common import topological_dimension
 from ._exceptions import ReadError, WriteError
 from ._helpers import (
     extension_to_filetype,

src/meshio/_common.py

@@ -83,72 +83,6 @@
     "tetra286": 286,
 }
 
-topological_dimension = {
-    "line": 1,
-    "triangle": 2,
-    "quad": 2,
-    "tetra": 3,
-    "hexahedron": 3,
-    "wedge": 3,
-    "pyramid": 3,
-    "line3": 1,
-    "triangle6": 2,
-    "quad9": 2,
-    "tetra10": 3,
-    "hexahedron27": 3,
-    "wedge18": 3,
-    "pyramid14": 3,
-    "vertex": 0,
-    "quad8": 2,
-    "hexahedron20": 3,
-    "triangle10": 2,
-    "triangle15": 2,
-    "triangle21": 2,
-    "line4": 1,
-    "line5": 1,
-    "line6": 1,
-    "tetra20": 3,
-    "tetra35": 3,
-    "tetra56": 3,
-    "quad16": 2,
-    "quad25": 2,
-    "quad36": 2,
-    "triangle28": 2,
-    "triangle36": 2,
-    "triangle45": 2,
-    "triangle55": 2,
-    "triangle66": 2,
-    "quad49": 2,
-    "quad64": 2,
-    "quad81": 2,
-    "quad100": 2,
-    "quad121": 2,
-    "line7": 1,
-    "line8": 1,
-    "line9": 1,
-    "line10": 1,
-    "line11": 1,
-    "tetra84": 3,
-    "tetra120": 3,
-    "tetra165": 3,
-    "tetra220": 3,
-    "tetra286": 3,
-    "wedge40": 3,
-    "wedge75": 3,
-    "hexahedron64": 3,
-    "hexahedron125": 3,
-    "hexahedron216": 3,
-    "hexahedron343": 3,
-    "hexahedron512": 3,
-    "hexahedron729": 3,
-    "hexahedron1000": 3,
-    "wedge126": 3,
-    "wedge196": 3,
-    "wedge288": 3,
-    "wedge405": 3,
-    "wedge550": 3,
-}
-
 
 def cell_data_from_raw(cells, cell_data_raw):
     cs = np.cumsum([len(c) for c in cells])[:-1]

src/meshio/_mesh.py

@@ -8,18 +8,97 @@
 
 from ._common import num_nodes_per_cell
 
+topological_dimension = {
+    "line": 1,
+    "polygon": 2,
+    "triangle": 2,
+    "quad": 2,
+    "tetra": 3,
+    "hexahedron": 3,
+    "wedge": 3,
+    "pyramid": 3,
+    "line3": 1,
+    "triangle6": 2,
+    "quad9": 2,
+    "tetra10": 3,
+    "hexahedron27": 3,
+    "wedge18": 3,
+    "pyramid14": 3,
+    "vertex": 0,
+    "quad8": 2,
+    "hexahedron20": 3,
+    "triangle10": 2,
+    "triangle15": 2,
+    "triangle21": 2,
+    "line4": 1,
+    "line5": 1,
+    "line6": 1,
+    "tetra20": 3,
+    "tetra35": 3,
+    "tetra56": 3,
+    "quad16": 2,
+    "quad25": 2,
+    "quad36": 2,
+    "triangle28": 2,
+    "triangle36": 2,
+    "triangle45": 2,
+    "triangle55": 2,
+    "triangle66": 2,
+    "quad49": 2,
+    "quad64": 2,
+    "quad81": 2,
+    "quad100": 2,
+    "quad121": 2,
+    "line7": 1,
+    "line8": 1,
+    "line9": 1,
+    "line10": 1,
+    "line11": 1,
+    "tetra84": 3,
+    "tetra120": 3,
+    "tetra165": 3,
+    "tetra220": 3,
+    "tetra286": 3,
+    "wedge40": 3,
+    "wedge75": 3,
+    "hexahedron64": 3,
+    "hexahedron125": 3,
+    "hexahedron216": 3,
+    "hexahedron343": 3,
+    "hexahedron512": 3,
+    "hexahedron729": 3,
+    "hexahedron1000": 3,
+    "wedge126": 3,
+    "wedge196": 3,
+    "wedge288": 3,
+    "wedge405": 3,
+    "wedge550": 3,
+    "VTK_LAGRANGE_CURVE": 1,
+    "VTK_LAGRANGE_TRIANGLE": 2,
+    "VTK_LAGRANGE_QUADRILATERAL": 2,
+    "VTK_LAGRANGE_TETRAHEDRON": 3,
+    "VTK_LAGRANGE_HEXAHEDRON": 3,
+    "VTK_LAGRANGE_WEDGE": 3,
+    "VTK_LAGRANGE_PYRAMID": 3,
+}
+
 
 class CellBlock:
     def __init__(
         self,
-        type: str,
+        cell_type: str,
         data: list | np.ndarray,
         tags: list[str] | None = None,
     ):
-        self.type = type
+        self.type = cell_type
         self.data = data
-        if not type.startswith("polyhedron"):
+
+        if cell_type.startswith("polyhedron"):
+            self.dim = 3
+        else:
             self.data = np.asarray(self.data)
+            self.dim = topological_dimension[cell_type]
+
         self.tags = [] if tags is None else tags
 
     def __repr__(self):

src/meshio/gmsh/_gmsh22.py

@@ -2,6 +2,8 @@
 I/O for Gmsh's msh format, cf.
 <http://gmsh.info//doc/texinfo/gmsh.html#File-formats>.
 """
+from __future__ import annotations
+
 import logging
 
 import numpy as np
@@ -128,7 +130,9 @@ def _read_cells(f, cells, point_tags, is_ascii):
         _read_cells_ascii(f, cells, cell_tags, total_num_cells)
     else:
         _read_cells_binary(f, cells, cell_tags, total_num_cells)
-    cells[:] = _gmsh_to_meshio_order(cells)
+
+    # override cells in-place
+    cells[:] = [(key, _gmsh_to_meshio_order(key, values)) for key, values in cells]
 
     point_tags = np.asarray(point_tags, dtype=np.int32) - 1
     remap = -np.ones((np.max(point_tags) + 1,), dtype=np.int32)
@@ -263,8 +267,6 @@ def write(filename, mesh, float_fmt=".16e", binary=True):
     """Writes msh files, cf.
     <http://gmsh.info//doc/texinfo/gmsh.html#MSH-ASCII-file-format>.
     """
-    cells = _meshio_to_gmsh_order(mesh.cells)
-
     # Filter the point data: gmsh:dim_tags are tags, the rest is actual point data.
     point_data = {}
     for key, d in mesh.point_data.items():
@@ -288,7 +290,9 @@ def write(filename, mesh, float_fmt=".16e", binary=True):
             logging.warning(
                 f"Appending zeros to replace the missing {tag[5:]} tag data."
             )
-            tag_data[tag] = [np.zeros(len(x.data), dtype=c_int) for x in mesh.cells]
+            tag_data[tag] = [
+                np.zeros(len(cell_block), dtype=c_int) for cell_block in mesh.cells
+            ]
 
     with open(filename, "wb") as fh:
         mode_idx = 1 if binary else 0
@@ -303,7 +307,7 @@ def write(filename, mesh, float_fmt=".16e", binary=True):
             _write_physical_names(fh, mesh.field_data)
 
         _write_nodes(fh, mesh.points, float_fmt, binary)
-        _write_elements(fh, cells, tag_data, binary)
+        _write_elements(fh, mesh.cells, tag_data, binary)
         if mesh.gmsh_periodic is not None:
             _write_periodic(fh, mesh.gmsh_periodic, float_fmt)
 
@@ -335,31 +339,18 @@ def _write_nodes(fh, points, float_fmt, binary):
     fh.write(b"$EndNodes\n")
 
 
-def _write_elements(fh, cells, tag_data, binary):
+def _write_elements(fh, cells: list[CellBlock], tag_data, binary: bool):
     # write elements
     fh.write(b"$Elements\n")
 
     # count all cells
-    total_num_cells = 0
-    for k, cell_block in enumerate(cells):
-        if isinstance(cell_block, tuple):
-            node_idcs = cell_block[1]
-        else:
-            assert isinstance(cell_block, CellBlock)
-            node_idcs = cell_block.data
-
-        total_num_cells += len(node_idcs)
-
+    total_num_cells = sum(len(cell_block) for cell_block in cells)
     fh.write(f"{total_num_cells}\n".encode())
 
     consecutive_index = 0
     for k, cell_block in enumerate(cells):
-        if isinstance(cell_block, tuple):
-            cell_type, node_idcs = cell_block
-        else:
-            assert isinstance(cell_block, CellBlock)
-            cell_type = cell_block.type
-            node_idcs = cell_block.data
+        cell_type = cell_block.type
+        node_idcs = _meshio_to_gmsh_order(cell_type, cell_block.data)
 
         tags = []
         for name in ["gmsh:physical", "gmsh:geometrical", "cell_tags"]: