Feature/additional geometry file export methods

coxeter/__init__.py

@@ -16,6 +16,8 @@
 applications such as inertia tensors.
 """
 
+from io import *
+
 from . import families, shapes
 from .shape_getters import from_gsd_type_shapes
 

coxeter/io.py

@@ -0,0 +1,278 @@
+import os
+import xml.etree.ElementTree as ET
+
+import numpy as np
+
+from coxeter import __version__
+
+
+def to_obj(shape, filename):
+    """Save shape to a wavefront OBJ file.
+
+    Args:
+        filename (str, pathlib.Path, or os.PathLike):
+            The name or path of the output file, including the extension.
+
+    Note:
+        In OBJ files, vertices in face definitions are indexed from one.
+
+    Raises
+    ------
+        OSError: If open() encounters a problem.
+    """
+    with open(filename, "w") as file:
+        file.write(
+            f"# wavefront obj file written by Coxeter "
+            f"version {__version__}\n"
+            f"# {shape.__class__.__name__}\n\n"
+        )
+
+        for v in shape.vertices:
+            file.write(f"v {' '.join([str(i) for i in v])}\n")
+
+        file.write("\n")
+
+        for f in shape.faces:
+            file.write(f"f {' '.join([str(i+1) for i in f])}\n")
+
+
+def to_off(shape, filename):
+    """Save shape to an Object File Format (OFF) file.
+
+    Args:
+        filename (str, pathlib.Path, or os.PathLike):
+            The name or path of the output file, including the extension.
+
+    Raises
+    ------
+        OSError: If open() encounters a problem.
+    """
+    with open(filename, "w") as file:
+        file.write(
+            f"OFF\n# OFF file written by Coxeter "
+            f"version {__version__}\n"
+            f"# {shape.__class__.__name__}\n"
+        )
+
+        file.write(
+            f"{len(shape.vertices)} f{len(shape.faces)} " f"{len(shape.edges)}\n"
+        )
+
+        for v in shape.vertices:
+            file.write(f"{' '.join([str(i) for i in v])}\n")
+
+        for f in shape.faces:
+            file.write(f"{len(f)} {' '.join([str(i) for i in f])}\n")
+
+
+def to_stl(shape, filename):
+    """Save shape to a stereolithography (STL) file.
+
+    Args:
+        filename (str, pathlib.Path, or os.PathLike):
+            The name or path of the output file, including the extension.
+
+    Note:
+        The output file is ASCII-encoded.
+
+    Raises
+    ------
+        OSError: If open() encounters a problem.
+    """
+    with open(filename, "w") as file:
+        # Shift vertices so all coordinates are positive
+        mins = np.amin(a=shape.vertices, axis=0)
+        for i, m in enumerate(mins):
+            if m < 0:
+                shape.centroid[i] -= m
+
+        # Write data
+        vs = shape.vertices
+        file.write(f"solid {shape.__class__.__name__}\n")
+
+        for f in shape.faces:
+            # Decompose face into triangles
+            # ref: https://stackoverflow.com/a/66586936/15426433
+            triangles = [[vs[f[0]], vs[b], vs[c]] for b, c in zip(f[1:], f[2:])]
+
+            for t in triangles:
+                n = np.cross(t[1] - t[0], t[2] - t[1])  # order?
+
+                file.write(f"facet normal {n[0]} {n[1]} {n[2]}\n" f"\touter loop\n")
+                for point in t:
+                    file.write(f"\t\tvertex {point[0]} {point[1]} {point[2]}\n")
+
+                file.write("\tendloop\nendfacet\n")
+
+        file.write(f"endsolid {shape.__class__.__name__}")
+
+
+def to_ply(shape, filename):
+    """Save shape to a Polygon File Format (PLY) file.
+
+    Args:
+        filename (str, pathlib.Path, or os.PathLike):
+            The name or path of the output file, including the extension.
+
+    Note:
+        The output file is ASCII-encoded.
+
+    Raises
+    ------
+        OSError: If open() encounters a problem.
+    """
+    with open(filename, "w") as file:
+        file.write(
+            f"ply\nformat ascii 1.0\n"
+            f"comment PLY file written by Coxeter "
+            f"version {__version__}\n"
+            f"comment {shape.__class__.__name__}\n"
+            f"element vertex {len(shape.vertices)}\n"
+            f"property float x\nproperty float y\nproperty float z\n"
+            f"element face {len(shape.faces)}\n"
+            f"property list uchar uint vertex_indices\n"
+            f"end_header\n"
+        )
+
+        for v in shape.vertices:
+            file.write(f"{' '.join([str(i) for i in v])}\n")
+
+        for f in shape.faces:
+            file.write(f"{len(f)} {' '.join([str(int(i)) for i in f])}\n")
+
+
+def to_x3d(shape, filename):
+    """Save shape to an Extensible 3D (X3D) file.
+
+    Args:
+        filename (str, pathlib.Path, or os.PathLike):
+            The name or path of the output file, including the extension.
+
+    Raises
+    ------
+        OSError: If open() encounters a problem.
+    """
+    # TODO: translate shape so that its centroid is at the origin
+
+    # Parent elements
+    root = ET.Element(
+        "x3d",
+        attrib={
+            "profile": "Interchange",
+            "version": "4.0",
+            "xmlns:xsd": "http://www.w3.org/2001/XMLSchema-instance",
+            "xsd:noNamespaceSchemaLocation": "http://www.web3d.org/specifications/x3d-4.0.xsd",
+        },
+    )
+    x3d_scene = ET.SubElement(root, "Scene")
+    x3d_shape = ET.SubElement(
+        x3d_scene, "shape", attrib={"DEF": f"{shape.__class__.__name__}"}
+    )
+
+    _ = ET.SubElement(x3d_shape, "Appearance")
+    _ = ET.SubElement(x3d_appearance, "Material", attrib={"diffuseColor": "#6495ED"})
+
+    # Geometry data
+    coordinate_indices = list(range(sum([len(f) for f in shape.faces])))
+    prev_index = 0
+    for f in shape.faces:
+        coordinate_indices.insert(len(f) + prev_index, -1)
+        prev_index += len(f) + 1
+
+    coordinate_points = [v for f in shape.faces for i in f for v in shape.vertices[i]]
+
+    x3d_indexedfaceset = ET.SubElement(
+        x3d_shape,
+        "IndexedFaceSet",
+        attrib={"coordIndex": " ".join([str(i) for i in coordinate_indices])},
+    )
+    x3d_coordinate = ET.SubElement(
+        x3d_indexedfaceset,
+        "Coordinate",
+        attrib={"point": " ".join([str(i) for i in coordinate_points])},
+    )
+
+    # Write to file
+    ET.ElementTree(root).write(filename, encoding="UTF-8")
+
+
+def to_vtk(shape, filename):
+    """Save shape to a legacy VTK file.
+
+    Args:
+        filename (str, pathlib.Path, or os.PathLike):
+            The name or path of the output file, including the extension.
+
+    Raises
+    ------
+        OSError: If open() encounters a problem.
+    """
+    content = ""
+    # Title and Header
+    content += (
+        f"# vtk DataFile Version 3.0\n"
+        f"{shape.__class__.__name__} created by "
+        f"Coxeter version {__version__}\n"
+        f"ASCII\n"
+    )
+
+    # Geometry
+    content += f"DATASET POLYDATA\n" f"POINTS {len(shape.vertices)} float\n"
+    for v in shape.vertices:
+        content += f"{v[0]} {v[1]} {v[2]}\n"
+
+    num_points = len(shape.faces)
+    num_connections = sum([len(f) for f in shape.faces])
+    content += f"POLYGONS {num_points} {num_points + num_connections}\n"
+    for f in shape.faces:
+        content += f"{len(f)} {' '.join([str(i) for i in f])}\n"
+
+    # Write file
+    with open(filename, "wb") as file:
+        file.write(content.encode("ascii"))
+
+
+def to_html(shape, filename):
+    """Save shape to an HTML file.
+
+    This method calls shape.to_x3d to create a temporary X3D file, then
+    parses that X3D file and creates an HTML file in its place.
+
+    Args:
+        filename (str, pathlib.Path, or os.PathLike):
+            The name or path of the output file, including the extension.
+
+    Raises
+    ------
+        OSError: If open() encounters a problem.
+    """
+    # Create, parse, and remove x3d file
+    to_x3d(shape, filename)
+    x3d = ET.parse(filename)
+    os.remove(filename)
+
+    # HTML Head
+    html = ET.Element("html")
+    head = ET.SubElement(html, "head")
+    script = ET.SubElement(
+        head,
+        "script",
+        attrib={"type": "text/javascript", "src": "http://x3dom.org/release/x3dom.js"},
+    )
+    script.text = " "  # ensures the tag is not shape-closing
+    link = ET.SubElement(
+        head,
+        "link",
+        attrib={
+            "rel": "stylesheet",
+            "type": "text/css",
+            "href": "http://x3dom.org/release/x3dom.css",
+        },
+    )
+
+    # HTML body
+    body = ET.SubElement(html, "body")
+    body.append(x3d.getroot())
+
+    # Write file
+    ET.ElementTree(html).write(filename, encoding="UTF-8")