Merge pull request #1086 from nschloe/polygons

Polygons

Author: nschloe

CHANGELOG.md

@@ -4,6 +4,13 @@ This document only describes _breaking_ changes in meshio. If you are interested
 fixes, enhancements etc., best follow [the meshio project on
 GitHub](https://github.com/nschloe/meshio).
 
+## v4.4.0 (Apr 29, 2021)
+
+- Polygons are now stored as `"polygon"` cell blocks, not `"polygonN"` (where `N` is the
+  number of nodes per polygon). One can simply retrieve the number of points via
+  `cellblock.data.shape[1]`.
+
+
 ## v4.0.0 (Feb 18, 2020)
 
 - `mesh.cells` used to be a dictionary of the form

meshio/_mesh.py

@@ -82,10 +82,24 @@ def __init__(
 
     def __repr__(self):
         lines = ["<meshio mesh object>", f"  Number of points: {len(self.points)}"]
+        special_cells = [
+            "polygon",
+            "polyhedron",
+            "VTK_LAGRANGE_CURVE",
+            "VTK_LAGRANGE_TRIANGLE",
+            "VTK_LAGRANGE_QUADRILATERAL",
+            "VTK_LAGRANGE_TETRAHEDRON",
+            "VTK_LAGRANGE_HEXAHEDRON",
+            "VTK_LAGRANGE_WEDGE",
+            "VTK_LAGRANGE_PYRAMID",
+        ]
         if len(self.cells) > 0:
             lines.append("  Number of cells:")
-            for tpe, elems in self.cells:
-                lines.append(f"    {tpe}: {len(elems)}")
+            for cell_type, elems in self.cells:
+                string = cell_type
+                if cell_type in special_cells:
+                    string += f"({elems.shape[1]})"
+                lines.append(f"    {string}: {len(elems)}")
         else:
             lines.append("  No cells.")
 

meshio/ply/_ply.py

@@ -43,25 +43,17 @@
 numpy_to_ply_dtype = {np.dtype(v): k for k, v in ply_to_numpy_dtype.items()}
 
 
-_cell_type_to_count = {"vertex": 1, "line": 2, "triangle": 3, "quad": 4}
-
-
-def cell_type_to_count(cell_type):
-    if cell_type in _cell_type_to_count:
-        return _cell_type_to_count[cell_type]
-
-    match = re.fullmatch(r"polygon(\d+)", cell_type)
-    if match:
-        return int(match.group(1))
-
-
-_cell_type_from_count = {val: key for (key, val) in _cell_type_to_count.items()}
-
-
 def cell_type_from_count(count):
-    """Reverse of ``cell_type_to_count``, defaults to ``"polygon" + str(counr)``
-    if unknown."""
-    return _cell_type_from_count.get(count) or "polygon" + str(count)
+    if count == 1:
+        return "vertex"
+    elif count == 2:
+        return "line"
+    elif count == 3:
+        return "triangle"
+    elif count == 4:
+        return "quad"
+
+    return "polygon"
 
 
 def read(filename):
@@ -145,7 +137,6 @@ def read_buffer(f):
                 f"got `{line}`"
             )
 
-    # read header
     if is_binary:
         mesh = _read_binary(
             f,
@@ -210,7 +201,7 @@ def _read_ascii(
     }
     cell_data = {}
 
-    # the faces must be read line-by-line
+    # polygons must be read line-by-line
     polygons = collections.defaultdict(list)
     for k in range(num_cells):
         line = f.readline().decode("utf-8").strip()
@@ -445,9 +436,11 @@ def write(filename, mesh, binary=True):  # noqa: C901
             pd.append(value)
 
         num_cells = 0
+        legal_cell_types = ["vertex", "line", "triangle", "quad", "polygon"]
         for cell_type, c in mesh.cells:
-            if cell_type_to_count(cell_type):
+            if cell_type in legal_cell_types:
                 num_cells += c.data.shape[0]
+
         if num_cells > 0:
             fh.write(f"element face {num_cells:d}\n".encode("utf-8"))
 
@@ -474,9 +467,7 @@ def write(filename, mesh, binary=True):  # noqa: C901
             if cell_dtype is not None:
                 ply_type = numpy_to_ply_dtype[cell_dtype]
                 fh.write(
-                    "property list {} {} vertex_indices\n".format(
-                        "uint8", ply_type
-                    ).encode("utf-8")
+                    f"property list uint8 {ply_type} vertex_indices\n".encode("utf-8")
                 )
 
         # TODO other cell data
@@ -489,7 +480,7 @@ def write(filename, mesh, binary=True):  # noqa: C901
 
             # cells
             for cell_type, data in mesh.cells:
-                if cell_type_to_count(cell_type) is None:
+                if cell_type not in legal_cell_types:
                     warnings.warn(
                         'cell_type "{}" is not supported by ply format - skipping'
                     )

meshio/vtk/_vtk.py

@@ -586,12 +586,17 @@ def translate_cells(data, types, cell_data_raw):
             cell = data[cell_idx]
 
             cell_type = vtk_to_meshio_type[vtk_cell_type]
-            if cell_type == "polygon":
-                cell_type += str(data[offsets[idx]])
 
-            if len(cells) > 0 and cells[-1].type == cell_type:
+            if (
+                len(cells) > 0
+                and cells[-1].type == cell_type
+                # the following check if needed for polygons; key can be equal, but
+                # still needs to go into a new block
+                and len(cell) == len(cells[-1].data[-1])
+            ):
                 cells[-1].data.append(cell)
             else:
+                # open up a new cell block
                 cells.append(CellBlock(cell_type, [cell]))
 
         # convert data to numpy arrays
@@ -752,15 +757,14 @@ def _write_cells(f, cells, binary):
     f.write(f"CELL_TYPES {total_num_cells}\n".encode("utf-8"))
     if binary:
         for c in cells:
-            key_ = c.type[:7] if c.type[:7] == "polygon" else c.type
-            vtk_type = meshio_to_vtk_type[key_]
+            vtk_type = meshio_to_vtk_type[c.type]
             np.full(len(c.data), vtk_type, dtype=np.dtype(">i4")).tofile(f, sep="")
         f.write(b"\n")
     else:
         # ascii
         for c in cells:
-            key_ = c.type[:7] if c.type[:7] == "polygon" else c.type
-            np.full(len(c.data), meshio_to_vtk_type[key_]).tofile(f, sep="\n")
+            vtk_type = meshio_to_vtk_type[c.type]
+            np.full(len(c.data), vtk_type).tofile(f, sep="\n")
             f.write(b"\n")
 
 

meshio/vtu/_vtu.py

@@ -97,7 +97,7 @@ def _cells_from_data(connectivity, offsets, types, cell_data_raw):
                     start_cn[items + 1],
                     _vtk_to_meshio_order(types[start], sz, dtype=offsets.dtype) - sz,
                 )
-                cells.append(CellBlock(meshio_type + str(sz), connectivity[indices]))
+                cells.append(CellBlock(meshio_type, connectivity[indices]))
 
                 # Store cell data for this set of cells
                 for name, d in cell_data_raw.items():
@@ -668,9 +668,10 @@ def write(filename, mesh, binary=True, compression="zlib", header_type=None):
     # in certain places.
     is_polyhedron_grid = False
     for c in mesh.cells:
-        if c.type[:10] == "polyhedron":
+        if c.type.startswith("polyhedron"):
             is_polyhedron_grid = True
             break
+
     # The current implementation cannot mix polyhedral cells with other cell types.
     # To write such meshes, represent all cells as polyhedra.
     if is_polyhedron_grid:
@@ -908,31 +909,9 @@ def _polyhedron_face_cells(face_cells):
 
         # types
         types_array = []
-        for k, v in mesh.cells:
-            # For polygon and polyhedron grids, the number of nodes is part of the cell
-            # type key. This part must be stripped away.
-            special_cells = [
-                "polygon",
-                "polyhedron",
-                "VTK_LAGRANGE_CURVE",
-                "VTK_LAGRANGE_TRIANGLE",
-                "VTK_LAGRANGE_QUADRILATERAL",
-                "VTK_LAGRANGE_TETRAHEDRON",
-                "VTK_LAGRANGE_HEXAHEDRON",
-                "VTK_LAGRANGE_WEDGE",
-                "VTK_LAGRANGE_PYRAMID",
-            ]
-            key_ = None
-            for string in special_cells:
-                if k.startswith(string):
-                    key_ = string
-
-            if key_ is None:
-                # No special treatment
-                key_ = k
-
-            # further adaptions for polyhedron
-            if k.startswith("polyhedron"):
+        for key, v in mesh.cells:
+            # some adaptions for polyhedron
+            if key.startswith("polyhedron"):
                 # Get face-cell relation on the vtu format. See comments in helper
                 # function for more information of how to specify this.
                 faces_loc, faceoffsets_loc = _polyhedron_face_cells(v)
@@ -944,8 +923,9 @@ def _polyhedron_face_cells(face_cells):
                 assert faces is not None
                 faces += faces_loc
                 faceoffsets += faceoffsets_loc
+                key = "polyhedron"
 
-            types_array.append(np.full(len(v), meshio_to_vtk_type[key_]))
+            types_array.append(np.full(len(v), meshio_to_vtk_type[key]))
 
         types = np.concatenate(
             types_array

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = meshio
-version = 4.3.13
+version = 4.4.0
 author = Nico Schlömer et al.
 author_email = [email protected]
 description = I/O for many mesh formats

test/helpers.py

@@ -254,8 +254,8 @@
     [
         ("triangle", [[0, 1, 2], [4, 5, 6]]),
         ("quad", [[0, 1, 2, 3]]),
-        ("polygon5", [[1, 4, 5, 6, 2]]),
-        ("polygon6", [[0, 3, 7, 8, 9, 10], [1, 3, 7, 8, 9, 10]]),
+        ("polygon", [[1, 4, 5, 6, 2]]),
+        ("polygon", [[0, 3, 7, 8, 9, 10], [1, 3, 7, 8, 9, 10]]),
     ],
 )
 

test/test_ply.py

@@ -17,6 +17,7 @@
         helpers.add_point_data(helpers.tri_mesh, 1, dtype=int),
         helpers.add_point_data(helpers.tri_mesh, 1, dtype=float),
         helpers.line_mesh,
+        helpers.polygon_mesh,
         # helpers.add_cell_data(helpers.tri_mesh, [("a", (), np.float64)]),
         # helpers.add_cell_data(helpers.tri_mesh, [("a", (2,), np.float64)]),
         # helpers.add_cell_data(helpers.tri_mesh, [("a", (3,), np.float64)]),