Add from_file and write_to_file to SpatialData

.typo-ci.yml

@@ -30,6 +30,7 @@ excluded_words:
   - shutil
   - functools
   - boltons
+  - meshio
   # matplotlib ----------------------------------
   - gca
   - mpl
@@ -118,6 +119,9 @@ excluded_words:
   - numpydoc
   # markdown / latex ----------------------------
   - cdot
+  # file extensions -----------------------------
+  - vtk
+  - stl
   # other ---------------------------------------
   - addopts
   - csm

CHANGELOG.md

@@ -79,6 +79,7 @@
   pending [ASDF #916](https://github.com/asdf-format/asdf/issues/916) [[#224]](https://github.com/BAMWelDX/weldx/pull/224)
 - set minimum Python version to 3.8 [[#229]](https://github.com/BAMWelDX/weldx/pull/229)[[#255]](https://github.com/BAMWelDX/weldx/pull/255)
 - only import some packages upon first use [[#247]](https://github.com/BAMWelDX/weldx/pull/247)
+- Add [meshio](https://pypi.org/project/meshio/) as new dependency [#265](https://github.com/BAMWelDX/weldx/pull/265)
 
 ## 0.2.2 (30.11.2020)
 

environment.yml

@@ -16,6 +16,7 @@ dependencies:
   - asdf>=2.7
   - openpyxl
   - fs
+  - meshio
   # graph packages
   - networkx
   # Code quality

setup.cfg

@@ -51,6 +51,7 @@ install_requires =
     fs
     ipywidgets
     k3d
+    meshio
 
 include_package_data = True
 

tests/test_geometry.py

@@ -2,6 +2,8 @@
 
 import copy
 import math
+from pathlib import Path
+from tempfile import TemporaryDirectory
 from typing import List, Union
 
 import numpy as np
@@ -2927,3 +2929,34 @@ def test_class_creation_exceptions(arguments, exception_type, test_name):
         """
         with pytest.raises(exception_type):
             SpatialData(*arguments)
+
+    @staticmethod
+    @pytest.mark.parametrize(
+        "filename",
+        ["test.ply", "test.stl", "test.vtk", Path("test.stl")],
+    )
+    def test_read_write_file(filename: Union[str, Path]):
+        """Test the `from_file` and `write_to_file` functions.
+
+        The test simply creates a `SpatialData` instance, writes it to a file and reads
+        it back. The result is compared to the original object.
+
+        Parameters
+        ----------
+        filename :
+            Name of the file
+
+        """
+        points = [[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]]
+        triangles = [[0, 1, 2], [2, 3, 0]]
+
+        data = SpatialData(points, triangles)
+        with TemporaryDirectory(dir=Path(__file__).parent) as tmpdirname:
+            filepath = f"{tmpdirname}/{filename}"
+            if isinstance(filename, Path):
+                filepath = Path(filepath)
+            data.write_to_file(filepath)
+            data_read = SpatialData.from_file(filepath)
+
+        assert np.allclose(data.coordinates, data_read.coordinates)
+        assert np.allclose(data.triangles, data_read.triangles)

weldx/geometry.py

@@ -4,8 +4,10 @@
 import copy
 import math
 from dataclasses import dataclass
+from pathlib import Path
 from typing import TYPE_CHECKING, Dict, List, Tuple, Union
 
+import meshio
 import numpy as np
 import pint
 from xarray import DataArray
@@ -2328,6 +2330,26 @@ def __post_init__(self):
             if not self.triangles.ndim == 2:
                 raise ValueError("SpatialData triangulation must be a 2d array")
 
+    @staticmethod
+    def from_file(file_name: Union[str, Path]) -> "SpatialData":
+        """Create an instance from a file.
+
+        Parameters
+        ----------
+        file_name :
+            Name of the source file.
+
+        Returns
+        -------
+        SpatialData:
+            New `SpatialData` instance
+
+        """
+        mesh = meshio.read(file_name)
+        triangles = mesh.cells_dict.get("triangle")
+
+        return SpatialData(mesh.points, triangles)
+
     @staticmethod
     def from_geometry_raster(geometry_raster: np.ndarray) -> "SpatialData":
         """Triangulate rasterized Geometry Profile.
@@ -2399,3 +2421,19 @@ def plot(
             label=label,
             show_wireframe=show_wireframe,
         )
+
+    def write_to_file(self, file_name: Union[str, Path]):
+        """Write spatial data into a file.
+
+        The extension prescribes the output format.
+
+        Parameters
+        ----------
+        file_name :
+            Name of the file
+
+        """
+        mesh = meshio.Mesh(
+            points=self.coordinates.data, cells={"triangle": self.triangles}
+        )
+        mesh.write(file_name)