capytaine 3.0.0a1__cp310-cp310-macosx_15_0_x86_64.whl

capytaine/meshes/io.py

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+# Copyright 2025 Mews Labs
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from typing import Union, Any, Optional
+from io import IOBase
+from pathlib import Path
+import tempfile
+import logging
+
+import numpy as np
+import xarray as xr
+
+from capytaine.tools.optional_imports import silently_import_optional_dependency
+from capytaine.meshes import Mesh, ReflectionSymmetricMesh
+
+meshio = silently_import_optional_dependency("meshio")
+trimesh = silently_import_optional_dependency("trimesh")
+
+LOG = logging.getLogger(__name__)
+
+_MESHIO_EXTS = {"inp", "msh", "avs", "cgns", "xml", "e", "exo", "f3grid", "h5m", "mdpa", "mesh", "meshb", "med", "bdf", "fem", "nas", "vol", "vol.gz", "obj", "off", "post", "post.gz", "dato", "dato.gz", "ply", "stl", "dat", "node", "ele", "svg", "su2", "ugrid", "vtk", "vtu", "wkt", "xdmf", "xmf", "gmsh"}
+
+_TRIMESH_EXTS = {"obj", "stl", "ply", "glb", "gltf", "off"}
+
+_XARRAY_EXTS = {"nc", "netcdf"}
+
+_BUILTIN_EXTS = {"pnl", "hst", "mar", "gdf", "nemoh", "wamit", "hydrostar", "hams"}
+
+_ALL_EXTS = _MESHIO_EXTS | _TRIMESH_EXTS | _XARRAY_EXTS | _BUILTIN_EXTS
+
+# Structure of the function calls:
+#
+#                                  load_mesh
+#                                  /     | \
+#                         if path /      |  \
+#                                /       |   \
+#                  _load_from_path       |    --------------------\
+#                    |         \         |                        |
+#                    |          \        | if opened file         | if object from external lib
+#   if implemented   |           \       |                        |
+#   by external lib  |         _read_mesh_from_file_like_object   |
+#                    |                   |  \                     |
+#                    |   if implemented  |   \ if built-in        |
+#                    |   by external lib |    \                   |
+#                    \                   |    _read_***           |
+#                     \                  |                        |
+#                      \                 |        ----------------/
+#                       \                |       /
+#                      _import_from_***_mesh_class
+#
+
+
+def load_mesh(mesh_to_be_loaded, file_format=None, *, backend=None) -> Union[Mesh, ReflectionSymmetricMesh]:
+    """Load a mesh from a file or file-like object.
+
+    This function can load mesh data from many file formats. It supports file
+    paths and file-like objects.
+
+    Parameters
+    ----------
+    mesh_to_be_loaded : str, pathlib.Path, or file-like object
+        Can be either:
+            - a path to a mesh file
+            - a file-like object with mesh file data
+            - a mesh object from one of the compatible external libraries (meshio, trimesh)
+    file_format : str, optional
+        Format hint used only when loading from file-like objects, since the
+        filename extension is unavailable.
+        Valid values include ``"stl"``, ``"obj"``, ``"hst"``, ``"pnl"``, etc.
+        Can be automatically inferred from file extension when a path is provided as first argument.
+
+    Returns
+    -------
+    Mesh or ReflectionSymmetricMesh
+        A Mesh object, or a ReflectionSymmetricMesh if symmetry information
+        is present in the file format.
+
+    Raises
+    ------
+    ValueError
+        If ``file_format`` is not provided when loading from a file-like
+        object, or if an unsupported format is encountered.
+
+    Examples
+    --------
+    Load a mesh from a file path.
+
+    >>> load_mesh("model.stl")
+
+    Load from a gzip-compressed file.
+
+    >>> import gzip
+    >>> with gzip.open("model.stl.gz") as handler:
+    ...     load_mesh(handler, file_format="stl")
+
+    Load from any file-like object.
+
+    >>> with open("model.obj", "rb") as handler:
+    ...     load_mesh(handler, file_format="obj")
+
+    """
+    if isinstance(mesh_to_be_loaded, IOBase):  # A file already opened
+        return _read_mesh_from_file_like_object(mesh_to_be_loaded, file_format, backend=backend)
+
+    elif backend in {None, "xarray"} and isinstance(mesh_to_be_loaded, xr.Dataset):
+        return _import_from_xarray_dataset(mesh_to_be_loaded)
+
+    elif trimesh is not None and backend in {None, "trimesh"} and isinstance(mesh_to_be_loaded, trimesh.base.Trimesh):
+        return _import_from_trimesh_mesh_class(mesh_to_be_loaded)
+
+    elif meshio is not None and backend in {None, "meshio"} and isinstance(mesh_to_be_loaded, meshio.Mesh):
+        return _import_from_meshio_mesh_class(mesh_to_be_loaded)
+
+    elif isinstance(mesh_to_be_loaded, (str, Path)):
+        return _load_from_path(Path(mesh_to_be_loaded), file_format, backend=backend)
+
+    else:
+        raise TypeError(f"load_mesh() can't interpret the type of input of {repr(mesh_to_be_loaded)}"
+                        + "" if backend is None else f" when using backend={backend}")
+
+
+
+def _normalise_format_hint(value: Any) -> str:
+    text = str(value).strip().lower()
+    if text.startswith("."):
+        text = text[1:]
+    return text
+
+
+def _load_from_path(path: Path, file_format: Optional[str] = None, *, backend: Optional[str] = None):
+    if not path.exists():
+        raise FileNotFoundError(f"Mesh file not found: {path}")
+
+    if file_format is None:
+        if len(path.suffixes) == 1:
+            file_format = path.suffixes[0]
+        else:
+            raise ValueError(f"No file format has been provided, nor can it be inferred from path: {path}")
+    fmt = _normalise_format_hint(file_format)
+
+    if trimesh is not None and backend in {None, "trimesh"} and fmt in _TRIMESH_EXTS:
+        trimesh_mesh = trimesh.load(path, force="mesh", file_type=fmt)
+        return _import_from_trimesh_mesh_class(trimesh_mesh)
+        # We could skip this, as _read_mesh_from_file_like_object would also try to pass the opened file to trimesh.
+        # However, some file format might supported by trimesh require the file to be opened in byte mode, and we don't want to handle that.
+
+    if meshio is not None and backend in {None, "meshio"} and fmt in _MESHIO_EXTS:
+        meshio_mesh = meshio.read(path, file_format=fmt)
+        return _import_from_meshio_mesh_class(meshio_mesh)
+        # We could skip this, as _read_mesh_from_file_like_object would also try to pass the opened file to meshio.
+        # But meshio does not support reading from an opened file, so we avoid the need for a temporary file by loading from the path here.
+
+    if backend in {None, "xarray"} and fmt in _XARRAY_EXTS:
+        dataset = xr.load_dataset(path)
+        return _import_from_xarray_dataset(dataset)
+
+    with open(path, 'r') as f:
+        return _read_mesh_from_file_like_object(f, file_format)
+
+
+def _read_mesh_from_file_like_object(
+    file_obj: IOBase,
+    file_format: str,
+    *,
+    backend: Optional[str] = None
+) -> Union[Mesh, ReflectionSymmetricMesh]:
+    fmt = _normalise_format_hint(file_format)
+
+    if fmt in _BUILTIN_EXTS and backend is None:
+        if fmt == "mar" or fmt == "nemoh":
+            return _read_mar(file_obj)
+        elif fmt == "gdf" or fmt == "wamit":
+            return _read_gdf(file_obj)
+        elif fmt == "hst" or fmt == "hydrostar":
+            return _read_hst(file_obj)
+        elif fmt == "pnl" or fmt == "hams":
+            return _read_pnl(file_obj)
+    elif trimesh is not None and backend in {None, "trimesh"} and fmt in _TRIMESH_EXTS:
+        trimesh_mesh = trimesh.load(file_obj, force="mesh", file_type=fmt)
+        return _import_from_trimesh_mesh_class(trimesh_mesh)
+    elif meshio is not None and backend in {None, "meshio"} and fmt in _MESHIO_EXTS:
+        # Meshio does not support reading from opened file, so it is written in a temporary file here
+        with tempfile.NamedTemporaryFile(delete=False) as temp_file:
+            content = file_obj.read()
+            if isinstance(content, str):
+                temp_file.write(content.encode("utf-8"))
+            else:
+                temp_file.write(content)
+        meshio_mesh = meshio.read(temp_file.name, file_format=fmt)
+        return _import_from_meshio_mesh_class(meshio_mesh)
+    elif backend in {None, "xarray"} and fmt in _XARRAY_EXTS:
+        # Seems to be supported according to documentation of xarray,
+        # but could not make it work with any backend in practice...
+        dataset = xr.load_dataset(file_obj)
+        return _import_from_xarray_dataset(dataset)
+    else:
+        raise ValueError(
+                f"Unrecognized or unsupported mesh format: {file_format}. "
+                f"Supported mesh formats (some may require external libraries to be installed): {sorted(_ALL_EXTS)}"
+        )
+
+
+def _import_from_meshio_mesh_class(meshio_mesh):
+    faces = []
+    if "quad" in meshio_mesh.cells_dict:
+        faces.extend(list(meshio_mesh.cells_dict["quad"]))
+    if "triangle" in meshio_mesh.cells_dict:
+        faces.extend(list(meshio_mesh.cells_dict["triangle"]))
+
+    if not faces:
+        raise ValueError("No triangle or quad cells found in meshio mesh.")
+
+    return Mesh(meshio_mesh.points, faces)
+
+
+def _import_from_trimesh_mesh_class(trimesh_mesh):
+    if not isinstance(trimesh_mesh, trimesh.base.Trimesh):
+        raise TypeError(f"Expected trimesh.base.Trimesh, received {type(trimesh_mesh)}")
+    return Mesh(trimesh_mesh.vertices, trimesh_mesh.faces)
+
+
+def _import_from_xarray_dataset(dataset):
+    return Mesh.from_list_of_faces(dataset["mesh_vertices"].values)
+
+
+def _read_hst(file_obj: IOBase) -> Union[Mesh, ReflectionSymmetricMesh]:
+    """HST files have a 1-based indexing"""
+
+    lines = file_obj.readlines()
+
+    optional_keywords = ['PROJECT', 'SYMMETRY']
+    not_implemented_optional_keywords = ['USER', 'REFLENGTH', 'GRAVITY', 'RHO', 'NBBODY']
+
+    vertices = []
+    faces = []
+    optional_data = {kw: None for kw in optional_keywords}
+    current_context = None
+    ignored_lines = []
+
+    for i_line, line in enumerate(lines):
+        line = line.lstrip()
+
+        if line == '':
+            continue
+
+        elif line.startswith("COORDINATES"):
+            current_context = 'vertices'
+
+        elif current_context == 'vertices' and line.startswith("ENDCOORDINATES"):
+            current_context = None
+
+        elif line.startswith("PANEL"):
+            panels_type = int(line[10:])
+            current_context = ('panels', panels_type)
+
+        elif (current_context == ('panels', 0) or current_context == ('panels', 1)) and line.startswith("ENDPANEL"):
+            current_context = None
+
+        elif current_context == 'vertices':  # parse vertex coordinates
+            numbers = line.split()
+            if len(numbers) == 4:
+                i_vertex, x, y, z = numbers
+                if int(i_vertex) != len(vertices) + 1:
+                    raise ValueError(
+                        f"HST mesh reader expected the next vertex to be indexed as {len(vertices)+1}, "
+                        f"but it was actually indexed as {i_vertex} (line {i_line+1}.")
+            elif len(numbers) == 3:
+                x, y, z = numbers
+            vertices.append([x, y, z])
+
+        elif current_context == ('panels', 0):  # parse face definition (no index given)
+            numbers = line.split()
+            if len(numbers) == 3:
+                v1, v2, v3 = numbers
+                v4 = v3
+            elif len(numbers) == 4:
+                v1, v2, v3, v4 = numbers
+            faces.append([v1, v2, v3, v4])
+
+        elif current_context == ('panels', 1):  # parse face definition
+            numbers = line.split()
+            if len(numbers) == 4:
+                i_face, v1, v2, v3 = numbers
+                v4 = v3
+            elif len(numbers) == 5:
+                i_face, v1, v2, v3, v4 = numbers
+
+            if int(i_face) != len(faces) + 1:
+                ii = len(faces) + 1
+                raise ValueError(f"HST mesh reader expected the next face to be indexed {ii},\n"
+                                 f"but it was actually indexed with {i_face} (line {i_line+1}.")
+            faces.append([v1, v2, v3, v4])
+
+        elif line.startswith("ENDFILE"):
+            break
+
+        else:
+            for keyword in optional_data:
+                if line.startswith(keyword):
+                    optional_data[keyword] = line[len(keyword)+1:].lstrip(':').strip()
+                    break
+            else:
+                ignored_lines.append((i_line+1, line))
+
+    if len(ignored_lines) > 0:
+        formatted_ignored_lines = ["{: 4} | {}".format(i, line.strip('\n')) for (i, line) in ignored_lines]
+        LOG.warning("HST mesh reader ignored the following lines:\n" + "\n".join(formatted_ignored_lines))
+
+    vertices = np.array(vertices, dtype=float)
+    faces = np.array(faces, dtype=int) - 1
+
+    if optional_data['SYMMETRY'] == '1':
+        return ReflectionSymmetricMesh(Mesh(vertices, faces), plane="xOz")
+    elif optional_data['SYMMETRY'] == '2':
+        return ReflectionSymmetricMesh(
+            ReflectionSymmetricMesh(Mesh(vertices, faces), plane="yOz"),
+            plane="xOz",
+        )
+    else:
+        return Mesh(vertices, faces)
+
+
+def _read_gdf(file_obj: IOBase) -> Union[Mesh, ReflectionSymmetricMesh]:
+    title = file_obj.readline()
+    ulen, grav = map(float, file_obj.readline().split()[:2])
+    isx, isy = map(int, file_obj.readline().split()[:2])
+    npan = int(file_obj.readline().split()[0])
+    faces_vertices = np.genfromtxt(file_obj)
+
+    faces_vertices = faces_vertices.reshape(-1, 3)
+    vertices, indices = np.unique(faces_vertices, axis=0, return_inverse=True)
+    faces = indices.reshape(-1, 4)
+
+    if faces.shape[0] != npan:
+        raise ValueError(
+            f"In GDF file, npan value: {npan} is not equal to face count: \
+                {faces.shape[0]}."
+        )
+
+    if isx == 1 and isy == 1:
+        return ReflectionSymmetricMesh(
+            ReflectionSymmetricMesh(Mesh(vertices, faces), plane="xOz"),
+            plane="yOz",
+        )
+    elif isx == 1:
+        return ReflectionSymmetricMesh(Mesh(vertices, faces), plane="yOz")
+    elif isy == 1:
+        return ReflectionSymmetricMesh(Mesh(vertices, faces), plane="xOz")
+    else:
+        return Mesh(vertices, faces)
+
+
+def _read_mar(file_obj) -> Union[Mesh, ReflectionSymmetricMesh]:
+    vertices = []
+    faces = []
+
+    # Read header: "n_faces symmetry_flag"
+    header = file_obj.readline().split()
+    symmetry_flag = int(header[1]) if len(header) > 1 else 0
+
+    # Read vertices until "0" marker
+    for line in file_obj:
+        tokens = line.split()
+        if tokens[0] == "0":
+            break
+        vertices.append(list(map(float, tokens[1:])))
+
+    # Read faces until "0" marker
+    for line in file_obj:
+        tokens = line.split()
+        if tokens[0] == "0":
+            break
+        faces.append(list(map(int, tokens)))
+
+    # Convert to numpy arrays and adjust indices (Fortran 1-based to Python 0-based)
+    vertices = np.array(vertices, dtype=float)
+    faces = np.array(faces, dtype=int) - 1
+
+    if symmetry_flag == 1:
+        return ReflectionSymmetricMesh(Mesh(vertices, faces), plane="xOz")
+    else:
+        return Mesh(vertices, faces)
+
+
+def _read_pnl(file_obj) -> Union[Mesh, ReflectionSymmetricMesh]:
+    # Skip 3 title lines
+    file_obj.readline()
+    file_obj.readline()
+    file_obj.readline()
+    # Read header data
+    nb_faces, nb_vertices, x_sym, y_sym = map(int, file_obj.readline().split())
+    # Skip 2 more lines
+    file_obj.readline()
+    file_obj.readline()
+    vertices = np.genfromtxt((file_obj.readline() for _ in range(nb_vertices)), usecols=(1, 2, 3))
+    # Skip 3 more lines
+    file_obj.readline()
+    file_obj.readline()
+    file_obj.readline()
+
+    faces = np.zeros((nb_faces, 4), dtype=int)
+    for i in range(nb_faces):
+        index, nb_corners, *data = map(int, file_obj.readline().split())
+        assert i+1 == index
+        if nb_corners == 3:  # Triangle
+            assert len(data) == 3
+            faces[i, 0:3] = data
+            faces[i, 3] = faces[i, 2]  # Convention for triangles in Capytaine: repeat last vertex
+        elif int(nb_corners) == 4:  # Quadrangle
+            assert len(data) == 4
+            faces[i, :] = data
+    faces = faces - 1  # Going from Fortran 1-based indices to Numpy 0-based indices
+
+    if x_sym == 1 and y_sym == 0:
+        return ReflectionSymmetricMesh(Mesh(vertices, faces), plane="yOz")
+    elif x_sym == 0 and y_sym == 1:
+        return ReflectionSymmetricMesh(Mesh(vertices, faces), plane="xOz")
+    elif x_sym == 1 and y_sym == 1:
+        half_mesh = ReflectionSymmetricMesh(Mesh(vertices, faces), plane="xOz")
+        return ReflectionSymmetricMesh(half_mesh, plane="yOz")
+    else:
+        return Mesh(vertices, faces)