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Implicit function clipping (#16)
* fix: add copy method and vtk method for trimesh object * chore: ignore windows build * fix: specify .so for unix and pyd for windows * ci: rename examples and adding test suite + git action * fix: adding option to cut surface with a property this is interpreted as a signed distance function and could be evaluated on the triangle nodes from an implicit function. Note if the surface is remeshed the property values will need to be re-evaluated on the new nodes. * fix: move checks to separate file and add import/export from np arrays * ci: use loop python versions (#15) * ci: adding windows/mac tests * ci: use c:: for vcpkg and revert to loop python env var * ci: use env var for mac as well * ci: update windows cmake instructions * Update environment variable for vcpkg toolchain Set VCPKG_ROOT environment variable for package build. * test: update test ci runner to use pypi runner template * tests: add cgal/eigen to nix * fix: specify python versions * fix: use exact meshes for clipping, avoid infinite hangs * fix: set default kernel to exact, use double for speed at risk of hanging ci: change name of tester to testing * Update examples/cut_example.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * [WIP] Add option to clip surface with implicit function (#17) * Initial plan * Address code review comments Co-authored-by: lachlangrose <7371904+lachlangrose@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: lachlangrose <7371904+lachlangrose@users.noreply.github.com> * fix: add dlls to package for wheel * tests: remove tmp files --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: lachlangrose <7371904+lachlangrose@users.noreply.github.com>
1 parent 566b392 commit 6cec095

17 files changed

Lines changed: 856 additions & 140 deletions

‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: ["**"]
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pull_request:
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branches: ["**"]
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jobs:
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tester:
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name: Testing
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest, macos-14,windows-latest]
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python-version: ${{ fromJSON(vars.PYTHON_VERSIONS)}}
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env:
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MACOSX_DEPLOYMENT_TARGET: '15.0'
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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- if: matrix.os == 'ubuntu-latest'
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run: |
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sudo apt-get install -y libgl1-mesa-dev libeigen3-dev libcgal-dev
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- if: ${{ startsWith(matrix.os, 'macos') }}
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run: |
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brew install cgal
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# Cache vcpkg on Windows
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- name: Restore vcpkg cache
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if: runner.os == 'Windows'
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id: cache-vcpkg
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uses: actions/cache@v4
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with:
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path: |
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C:/vcpkg
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key: vcpkg-${{ runner.os }}-${{ hashFiles('vcpkg.json') }}
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restore-keys: |
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vcpkg-${{ runner.os }}-
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- name: Install vcpkg dependencies (Windows only)
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if: runner.os == 'Windows'
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shell: pwsh
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run: |
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$Env:VCPKG_ROOT = "C:/vcpkg"
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if (!(Test-Path $Env:VCPKG_ROOT)) {
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git clone https://github.com/microsoft/vcpkg $Env:VCPKG_ROOT
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& "$Env:VCPKG_ROOT/bootstrap-vcpkg.bat"
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}
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# Only install if packages are missing
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if (!(Test-Path "$Env:VCPKG_ROOT/installed/x64-windows/cgal")) {
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& "$Env:VCPKG_ROOT/vcpkg.exe" install yasm-tool cgal
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}
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echo "VCPKG_ROOT=$Env:VCPKG_ROOT" >> $Env:GITHUB_ENV
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# now inject your extra CMake flags:
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$toolchain = "$Env:VCPKG_ROOT/scripts/buildsystems/vcpkg.cmake"
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echo "CMAKE_ARGS=-DCMAKE_TOOLCHAIN_FILE=${toolchain} -DVCPKG_ROOT=${Env:VCPKG_ROOT}" >> $Env:GITHUB_ENV
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echo $CMAKE_ARGS
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- name: Pip install
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run: |
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pip install .[test]
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- name: Run tests
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run: |
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pytest
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‎.gitignore‎

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@@ -43,4 +43,5 @@ Thumbs.db
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loop_cgal/__pycache__/__init__.cpython-311.pyc
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build/*
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*.vtk
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*.ply
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*.ply
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build_win64/*

‎CMakeLists.txt‎

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Original file line numberDiff line numberDiff line change
@@ -25,26 +25,30 @@ add_library(_loop_cgal MODULE
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target_link_libraries(_loop_cgal PRIVATE pybind11::module CGAL::CGAL)
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target_include_directories(_loop_cgal PRIVATE ${CMAKE_SOURCE_DIR}/src)
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set_target_properties(_loop_cgal PROPERTIES PREFIX "" SUFFIX ".pyd")
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if(WIN32)
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set_target_properties(_loop_cgal PROPERTIES PREFIX "" SUFFIX ".pyd")
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else()
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set_target_properties(_loop_cgal PROPERTIES PREFIX "" SUFFIX ".so")
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endif()
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# Windows: copy required DLLs from VCPKG_ROOT
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if(WIN32)
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if(NOT DEFINED ENV{VCPKG_ROOT})
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message(FATAL_ERROR "VCPKG_ROOT environment variable is not set!")
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endif()
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set(VCPKG_ROOT $ENV{VCPKG_ROOT})
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message(STATUS "Using VCPKG_ROOT: ${VCPKG_ROOT}")
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add_custom_command(TARGET _loop_cgal POST_BUILD
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COMMAND ${CMAKE_COMMAND} -E copy_if_different
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"${VCPKG_ROOT}/packages/gmp_x64-windows/bin/gmp-10.dll"
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"$<TARGET_FILE_DIR:_loop_cgal>"
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COMMAND ${CMAKE_COMMAND} -E copy_if_different
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"${VCPKG_ROOT}/packages/mpfr_x64-windows/bin/mpfr-6.dll"
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"$<TARGET_FILE_DIR:_loop_cgal>"
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)
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install(CODE "
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file(INSTALL
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DESTINATION \"\${CMAKE_INSTALL_PREFIX}/loop_cgal\"
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TYPE FILE
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FILES
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\"${VCPKG_ROOT}/packages/gmp_x64-windows/bin/gmp-10.dll\"
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\"${VCPKG_ROOT}/packages/mpfr_x64-windows/bin/mpfr-6.dll\"
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)
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message(\"[CMake Install] Copied gmp-10.dll and mpfr-6.dll to install directory.\")
47+
")
4648
endif()
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4852
# Install for Python packages
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install(TARGETS _loop_cgal
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LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/loop_cgal

examples/clip_test.py renamed to examples/clip_example.py

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‎examples/cut_example.py‎

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import numpy as np
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from loop_cgal import TriMesh, set_verbose
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from LoopStructural.datatypes import BoundingBox
4+
set_verbose(True)
5+
6+
7+
bb = BoundingBox(np.zeros(3), np.ones(3))
8+
grid = bb.structured_grid().vtk()
9+
grid["scalars"] = grid.points[:, 0]
10+
surface = grid.contour([0.5])
11+
property = surface.points[:, 1].copy()
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surface['prop'] = property
13+
surface.save("input_mesh.vtk")
14+
15+
mesh = TriMesh(surface)
16+
17+
# Define a scalar property that is the Y coordinate of each vertex
18+
19+
# Cut value at y = 0.6; this will split triangles crossing y=0.6
20+
cut_value = property.mean()
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# mesh.remesh(0.10, protect_constraints=False)
22+
23+
mesh.vtk().save('before_cut.vtk')
24+
# Invoke the new method (property is python list or numpy array)
25+
mesh.cut_with_implicit_function(property.tolist(), cut_value)
26+
mesh.reverse_face_orientation()
27+
# Convert back to pyvista for visualization
28+
out = mesh.to_pyvista()
29+
out.save('cut_mesh.vtk')
30+
# # Visualize the result
31+
# pl = pv.Plotter()
32+
# pl.add_mesh(out, show_edges=True, color='lightgray')
33+
# pl.add_mesh(pv.PolyData(np.array([[cut_value, -1e3, 0.0],[cut_value,1e3,0.0]])), color='red')
34+
# pl.show()

examples/split_test.py renamed to examples/split_example.py

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‎loop_cgal/__init__.py‎

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Original file line numberDiff line numberDiff line change
@@ -7,104 +7,86 @@
77
import pyvista as pv
88

99
from ._loop_cgal import TriMesh as _TriMesh
10-
from ._loop_cgal import verbose # noqa: F401
10+
from ._loop_cgal import verbose # noqa: F401
1111
from ._loop_cgal import set_verbose as set_verbose
1212

13-
14-
15-
16-
17-
def validate_pyvista_polydata(surface: pv.PolyData, surface_name: str = "surface") -> None:
18-
"""Validate a PyVista PolyData object.
19-
20-
Parameters
21-
----------
22-
surface : pv.PolyData
23-
The surface to validate
24-
surface_name : str
25-
Name of the surface for error messages
26-
27-
Raises
28-
------
29-
ValueError
30-
If the surface is invalid
31-
"""
32-
if not isinstance(surface, pv.PolyData):
33-
raise ValueError(f"{surface_name} must be a pyvista.PolyData object")
34-
35-
if surface.n_points == 0:
36-
raise ValueError(f"{surface_name} has no points")
37-
38-
if surface.n_cells == 0:
39-
raise ValueError(f"{surface_name} has no cells")
40-
41-
points = np.asarray(surface.points)
42-
if not np.isfinite(points).all():
43-
raise ValueError(f"{surface_name} points contain NaN or infinite values")
44-
13+
from .utils import validate_pyvista_polydata, validate_vertices_and_faces
4514

4615

4716
class TriMesh(_TriMesh):
4817
"""
4918
A class for handling triangular meshes using CGAL.
50-
19+
5120
Inherits from the base TriMesh class and provides additional functionality.
5221
"""
22+
5323
def __init__(self, surface: pv.PolyData):
5424
# Validate input surface
5525
validate_pyvista_polydata(surface, "input surface")
56-
26+
5727
# Triangulate to ensure we have triangular faces
5828
surface = surface.triangulate()
59-
29+
6030
# Extract vertices and triangles
6131
verts = np.array(surface.points, dtype=np.float64).copy()
6232
faces = surface.faces.reshape(-1, 4)[:, 1:].copy().astype(np.int32)
63-
64-
# Additional validation on extracted data
65-
if verts.size == 0:
66-
raise ValueError("Surface has no vertices after triangulation")
67-
68-
if faces.size == 0:
69-
raise ValueError("Surface has no triangular faces after triangulation")
70-
71-
if not np.isfinite(verts).all():
72-
raise ValueError("Surface vertices contain NaN or infinite values")
73-
74-
# Check triangle indices
75-
max_vertex_index = verts.shape[0] - 1
76-
if faces.min() < 0:
77-
raise ValueError("Surface has negative triangle indices")
78-
79-
if faces.max() > max_vertex_index:
80-
raise ValueError(f"Surface triangle indices exceed vertex count (max index: {faces.max()}, vertex count: {verts.shape[0]})")
81-
# Check for degenerate triangles
82-
# build a ntris x nverts matrix
83-
# populate with true for vertex in each triangle
84-
# sum rows and if not equal to 3 then it is degenerate
85-
face_idx = np.arange(faces.shape[0])
86-
face_idx = np.tile(face_idx, (3,1)).T.flatten()
87-
faces_flat = faces.flatten()
88-
m = sp.coo_matrix(
89-
(np.ones(faces_flat.shape[0]), (faces_flat, face_idx)),
90-
shape=(verts.shape[0], faces.shape[0]),
91-
dtype=bool,
92-
)
93-
# coo duplicates entries so just make sure its boolean
94-
m = m > 0
95-
if not np.all(m.sum(axis=0) == 3):
96-
degen_idx = np.where(m.sum(axis=0) != 3)[1]
97-
raise ValueError(f"Surface contains degenerate triangles: {degen_idx} (each triangle must have exactly 3 vertices)")
98-
33+
if not validate_vertices_and_faces(verts, faces):
34+
raise ValueError("Invalid surface geometry")
9935

10036
super().__init__(verts, faces)
101-
102-
def to_pyvista(self, area_threshold: float = 1e-6, # this is the area threshold for the faces, if the area is smaller than this it will be removed
103-
duplicate_vertex_threshold: float = 1e-4, # this is the threshold for duplicate vertices
104-
) -> pv.PolyData:
37+
@classmethod
38+
def from_vertices_and_triangles(
39+
cls, vertices: np.ndarray, triangles: np.ndarray
40+
) -> TriMesh:
41+
"""
42+
Create a TriMesh from vertices and triangle indices.
43+
44+
Parameters
45+
----------
46+
vertices : np.ndarray
47+
An array of shape (n_vertices, 3) containing the vertex coordinates.
48+
triangles : np.ndarray
49+
An array of shape (n_triangles, 3) containing the triangle vertex indices.
50+
51+
Returns
52+
-------
53+
TriMesh
54+
The created TriMesh object.
55+
"""
56+
# Create a temporary PyVista PolyData object for validation
57+
if not validate_vertices_and_faces(vertices, triangles):
58+
raise ValueError("Invalid vertices or triangles")
59+
surface = pv.PolyData(vertices, np.hstack((np.full((triangles.shape[0], 1), 3), triangles)).flatten())
60+
return cls(surface)
61+
62+
def get_vertices_and_triangles(
63+
self,
64+
area_threshold: float = 1e-6, # this is the area threshold for the faces, if the area is smaller than this it will be removed
65+
duplicate_vertex_threshold: float = 1e-4,
66+
) -> Tuple[np.ndarray, np.ndarray]:
67+
"""
68+
Get the vertices and triangle indices of the TriMesh.
69+
70+
Returns
71+
-------
72+
Tuple[np.ndarray, np.ndarray]
73+
A tuple containing:
74+
- An array of shape (n_vertices, 3) with the vertex coordinates.
75+
- An array of shape (n_triangles, 3) with the triangle vertex indices.
76+
"""
77+
np_mesh = self.save(area_threshold, duplicate_vertex_threshold)
78+
vertices = np.array(np_mesh.vertices).copy()
79+
triangles = np.array(np_mesh.triangles).copy()
80+
return vertices, triangles
81+
82+
def to_pyvista(
83+
self,
84+
area_threshold: float = 1e-6, # this is the area threshold for the faces, if the area is smaller than this it will be removed
85+
duplicate_vertex_threshold: float = 1e-4, # this is the threshold for duplicate vertices
86+
) -> pv.PolyData:
10587
"""
10688
Convert the TriMesh to a pyvista PolyData object.
107-
89+
10890
Returns
10991
-------
11092
pyvista.PolyData
@@ -115,3 +97,23 @@ def to_pyvista(self, area_threshold: float = 1e-6, # this is the area threshold
11597
triangles = np.array(np_mesh.triangles).copy()
11698
return pv.PolyData.from_regular_faces(vertices, triangles)
11799

100+
def vtk(
101+
self,
102+
area_threshold: float = 1e-6,
103+
duplicate_vertex_threshold: float = 1e-4,
104+
) -> pv.PolyData:
105+
"""
106+
Alias for to_pyvista method.
107+
"""
108+
return self.to_pyvista(area_threshold, duplicate_vertex_threshold)
109+
110+
def copy(self) -> TriMesh:
111+
"""
112+
Create a copy of the TriMesh.
113+
114+
Returns
115+
-------
116+
TriMesh
117+
A copy of the TriMesh object.
118+
"""
119+
return TriMesh(self.to_pyvista())

‎loop_cgal/bindings.cpp‎

Lines changed: 11 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -14,12 +14,18 @@ PYBIND11_MODULE(_loop_cgal, m)
1414
.def(py::init<>())
1515
.def_readwrite("vertices", &NumpyMesh::vertices)
1616
.def_readwrite("triangles", &NumpyMesh::triangles);
17+
py::enum_<ImplicitCutMode>(m, "ImplicitCutMode")
18+
.value("PRESERVE_INTERSECTION", ImplicitCutMode::PRESERVE_INTERSECTION)
19+
.value("KEEP_POSITIVE_SIDE", ImplicitCutMode::KEEP_POSITIVE_SIDE)
20+
.value("KEEP_NEGATIVE_SIDE", ImplicitCutMode::KEEP_NEGATIVE_SIDE)
21+
.export_values();
1722
py::class_<TriMesh>(m, "TriMesh")
1823
.def(py::init<const pybind11::array_t<double> &, const pybind11::array_t<int> &>(),
1924
py::arg("vertices"), py::arg("triangles"))
2025
.def("cut_with_surface", &TriMesh::cutWithSurface, py::arg("surface"),
2126
py::arg("preserve_intersection") = false,
22-
py::arg("preserve_intersection_clipper") = false)
27+
py::arg("preserve_intersection_clipper") = false,
28+
py::arg("use_exact_kernel") = true)
2329
.def("remesh", &TriMesh::remesh, py::arg("split_long_edges") = true,
2430
py::arg("target_edge_length") = 10.0,
2531
py::arg("number_of_iterations") = 3,
@@ -31,6 +37,9 @@ PYBIND11_MODULE(_loop_cgal, m)
3137
"Reverse the face orientation of the mesh.")
3238
.def("add_fixed_edges", &TriMesh::add_fixed_edges,
3339
py::arg("pairs"),
34-
"Vertex index pairs defining edges to be fixed in mesh when remeshing.");
40+
"Vertex index pairs defining edges to be fixed in mesh when remeshing.")
41+
.def("cut_with_implicit_function", &TriMesh::cut_with_implicit_function,
42+
py::arg("property"), py::arg("value"),py::arg("cutmode") = ImplicitCutMode::KEEP_POSITIVE_SIDE,
43+
"Cut the mesh with an implicit function defined by vertex properties.");
3544

3645
} // End of PYBIND11_MODULE

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