Merge pull request #75 from fwilliams/update_numpyeigen

fwilliams · Sep 10, 2023 · cf0c166 · cf0c166
2 parents 2ff54e9 + 0526892
commit cf0c166
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Showing 27 changed files with 59 additions and 59 deletions.
diff --git a/.vscode/c_cpp_properties.json b/.vscode/c_cpp_properties.json
@@ -15,7 +15,8 @@
                 "${workspaceFolder}/external/geogram/src/lib",
                 "${workspaceFolder}/src",
                 "${workspaceFolder}/external",
-                "${env:CONDA_PREFIX}/envs/point-cloud-utils/include/python3.9"
+                "${env:CONDA_PREFIX}/envs/point-cloud-utils/include/python3.10",
+                "${env:CONDA_PREFIX}/envs/point-cloud-utils/lib/python3.10/site-packages/numpy/core/include/"
             ],
             "macFrameworkPath": [
                 "${default}"

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -33,7 +33,7 @@ set(EXTERNAL_DEP_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external)
 include(DownloadExternalDeps)
 download_dep(numpyeigen
   GIT_REPOSITORY https://github.com/fwilliams/numpyeigen.git
-  GIT_TAG 70f3f100f23e9fc5888edcfd9ad38312b222c7ea
+  GIT_TAG master
 )
 list(APPEND CMAKE_MODULE_PATH ${EXTERNAL_DEP_DIR}/numpyeigen/cmake)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)

diff --git a/point_cloud_utils/_point_cloud_geometry.py b/point_cloud_utils/_point_cloud_geometry.py
@@ -45,14 +45,13 @@ def _validate_point_radius_internal(p, r):
 def voxel_grid_geometry(ijk, voxel_size=np.array((1., 1., 1.)), voxel_origin=np.array((0., 0., 0.)), gap_fraction=0.0):
     """
     Generate a triangle mesh of cubes for voxel coordinates ijk. The [0, 0, 0] voxel has its
-    bottom-back-left corner at voxel_origin and each voxel has voxel_size.
+    center at voxel_origin and each voxel has voxel_size.
 
     Args:
         ijk np.ndarray: [num_voxels, 3] array of integer voxel coordinates
         voxel_size: Float or triple representing the size of each voxel.
                     Defaults to np.array((1., 1., 1.)).
-        voxel_origin: Bottom-back-left coordinate of the [0, 0, 0] voxel.
-                      Defaults to np.array((0., 0., 0.)).
+        voxel_origin: Center coordinate of the [0, 0, 0] voxel. Defaults to np.array((0., 0., 0.)).
         gap_fraction: Fraction of a voxel to leave as a gap between voxels (default 0.0)
 
     Returns:

diff --git a/src/closest_point_on_mesh.cpp b/src/closest_point_on_mesh.cpp
@@ -25,7 +25,7 @@ Compute distances from a set of points p to a triangle mesh (v, f)
 npe_function(closest_points_on_mesh)
 npe_arg(p, dense_float, dense_double)
 npe_arg(v, npe_matches(p))
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_doc(closest_points_on_mesh_doc)
 npe_begin_code()
 {

diff --git a/src/connected_components.cpp b/src/connected_components.cpp
@@ -82,7 +82,7 @@ Determine the connected components of a mesh
 npe_function(connected_components)
 npe_doc(connected_components_doc)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_long, dense_longlong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_begin_code()
 {
     Eigen::SparseMatrix<npe_Scalar_f> A;

diff --git a/src/curvature.cpp b/src/curvature.cpp
@@ -45,7 +45,7 @@ Estimate principal curvature directions and magnitudes for a mesh
 )Qu8mg5v7";
 npe_function(mesh_principal_curvatures)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_long, dense_longlong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_default_arg(r, double, -1.0)
 npe_doc(mesh_principal_curvatures_doc)
 npe_begin_code()
@@ -94,7 +94,7 @@ npe_end_code()
 //)Qu8mg5v7";
 //npe_function(mesh_mean_and_gaussian_curvatures)
 //npe_arg(v, dense_float, dense_double)
-//npe_arg(f, dense_int, dense_long, dense_longlong)
+//npe_arg(f, dense_int32, dense_int64)
 //npe_doc(mesh_mean_and_gaussian_curvatures_doc)
 //npe_begin_code()
 //{
@@ -122,7 +122,7 @@ npe_end_code()
 //)Qu8mg5v7";
 //npe_function(pointcloud_apss_curvature)
 //npe_arg(v, dense_float, dense_double)
-//npe_arg(f, dense_int, dense_long, dense_longlong)
+//npe_arg(f, dense_int32, dense_int64)
 //npe_doc(pointcloud_apss_curvature_doc)
 //npe_begin_code()
 //{

diff --git a/src/face_areas.cpp b/src/face_areas.cpp
@@ -16,7 +16,7 @@ Compute the areas of each face of a triangle mesh
 )Qu8mg5v7";
 npe_function(mesh_face_areas)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_long, dense_longlong)
+npe_arg(f, dense_int32, dense_int64)
 npe_default_arg(num_threads, int, -1)
 npe_doc(triangle_mesh_face_areas_doc)
 npe_begin_code()

diff --git a/src/fast_winding_numbers.cpp b/src/fast_winding_numbers.cpp
@@ -19,7 +19,7 @@ at a set of query points
 )igl_Qu8mg5v7";
 npe_function(triangle_soup_fast_winding_number)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_long, dense_longlong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(p, npe_matches(v))
 npe_doc(triangle_soup_fast_winding_number_doc)
 npe_begin_code()

diff --git a/src/flood_fill_3d.cpp b/src/flood_fill_3d.cpp
@@ -53,7 +53,7 @@ void flood_fill(EigenMat& grid,
 
 
 npe_function(_flood_fill_3d_internal)
-npe_arg(grid, dense_int, dense_long, dense_longlong, dense_float, dense_double)
+npe_arg(grid, dense_int32, dense_int64, dense_float, dense_double)
 npe_arg(seed_x, int)
 npe_arg(seed_y, int)
 npe_arg(seed_z, int)

diff --git a/src/lloyd.cpp b/src/lloyd.cpp
@@ -356,7 +356,7 @@ Lloyd's algorithm (https://en.wikipedia.org/wiki/Lloyd%27s_algorithm).
 
 npe_function(sample_mesh_lloyd)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_long, dense_longlong, dense_uint, dense_ulong, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(num_samples, int)
 npe_default_arg(num_lloyd, int, 10)
 npe_default_arg(num_newton, int, 10)

diff --git a/src/manifold.cpp b/src/manifold.cpp
@@ -18,7 +18,7 @@ Convert a mesh into a watertight manifold using the [Manifold](https://arxiv.org
 )igl_Qu8mg5v7";
 npe_function(make_mesh_watertight)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_long, dense_longlong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_default_arg(resolution, double, 20000)
 npe_default_arg(seed, int, -1)
 npe_doc(make_mesh_watertight_doc)

diff --git a/src/marching_cubes.cpp b/src/marching_cubes.cpp
@@ -35,7 +35,7 @@ See Also:
 npe_function(marching_cubes_sparse_voxel_grid)
 npe_arg(grid_scalars, dense_float, dense_double)
 npe_arg(grid_coordinates, dense_float, dense_double)
-npe_arg(cube_indices, dense_int, dense_long, dense_longlong)
+npe_arg(cube_indices, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(isovalue, double)
 npe_doc(marching_cubes_sparse_voxel_grid_doc)
 npe_begin_code()

diff --git a/src/mesh_decimate.cpp b/src/mesh_decimate.cpp
@@ -22,7 +22,7 @@ Decimate a (manifold) triangle mesh by collapsing edges
 )Qu8mg5v7";
 npe_function(decimate_triangle_mesh)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_long, dense_longlong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(max_faces, int)
 npe_default_arg(decimation_heuristic, std::string, "shortest_edge")
 npe_doc(decimate_triangle_mesh_doc)

diff --git a/src/mesh_for_voxels.cpp b/src/mesh_for_voxels.cpp
@@ -13,7 +13,6 @@ namespace {
                             const MatrixIJK& in_ijk,
                             Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>& out_v,
                             Eigen::Matrix<int, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>& out_f) {
-
         std::array<int, 36> indices = {
             //Top
             2, 7, 6,
@@ -60,7 +59,7 @@ namespace {
                 Eigen::Vector3d vertex(vertices[vi * 3 + 0] * (1.0 - gap_fraction) + 0.5 * gap_fraction,
                                        vertices[vi * 3 + 1] * (1.0 - gap_fraction) + 0.5 * gap_fraction,
                                        vertices[vi * 3 + 2] * (1.0 - gap_fraction) + 0.5 * gap_fraction);
-                Eigen::Vector3d voxel_translation(in_ijk(i, 0), in_ijk(i, 1), in_ijk(i, 2));
+                Eigen::Vector3d voxel_translation((double) in_ijk(i, 0), (double) in_ijk(i, 1), (double) in_ijk(i, 2));
                 vertex += voxel_translation;
                 vertex.array() *= vox_size.array();
                 vertex += vox_origin;
@@ -82,10 +81,10 @@ namespace {
 
 
 npe_function(_voxel_mesh_internal)
-npe_arg(ijk, dense_int, dense_long, dense_longlong)
+npe_arg(ijk, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(gap_fraction, double)
-npe_arg(vox_origin, dense_double)
-npe_arg(vox_size, dense_double)
+npe_arg(vox_origin, dense_float, dense_double)
+npe_arg(vox_size, dense_float, dense_double)
 npe_begin_code()
     using MatrixI = Eigen::Matrix<int, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;
     using MatrixF = Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;
@@ -99,12 +98,12 @@ npe_begin_code()
         throw pybind11::value_error("Invalid shape");
     }
 
-    Eigen::Vector3d vsize = vox_size;
+    Eigen::Vector3d vsize = vox_size.template cast<double>();
 
     if (vsize[0] <= 0.0 || vsize[1] <= 0.0 || vsize[2] <= 0.0) {
         throw pybind11::value_error("Voxel size must be positive");
     }
-    Eigen::Vector3d vorgn = vox_origin;
+    Eigen::Vector3d vorgn = vox_origin.template cast<double>();
 
     MatrixF geom_vertices;
     MatrixI geom_faces;

diff --git a/src/mesh_normals.cpp b/src/mesh_normals.cpp
@@ -24,7 +24,7 @@ Compute vertex normals of a mesh from its vertices and faces using face area wei
 npe_function(estimate_mesh_vertex_normals)
 npe_doc(estimate_mesh_vertex_normals_doc)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_default_arg(weighting_type, std::string, std::string("uniform"))
 npe_begin_code()
 {
@@ -65,7 +65,7 @@ Compute vertex normals of a mesh from its vertices and faces using face area wei
 npe_function(estimate_mesh_face_normals)
 npe_doc(estimate_mesh_face_normals_doc)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_begin_code()
 {
     validate_mesh(v, f);

diff --git a/src/morton.cpp b/src/morton.cpp
@@ -24,8 +24,8 @@ Add morton codes together (corresponding to adding the vectors they encode)
 
 )Qu8mg5v7";
 npe_function(morton_add)
-npe_arg(codes_1, dense_uint, dense_ulong, dense_ulonglong)
-npe_arg(codes_2, dense_uint, dense_ulong, dense_ulonglong)
+npe_arg(codes_1, dense_uint32, dense_uint64)
+npe_arg(codes_2, dense_uint32, dense_uint64)
 npe_default_arg(num_threads, int, -1)
 npe_doc(morton_add)
 npe_begin_code()
@@ -104,8 +104,8 @@ Subtract morton codes from each other (corresponding to adding the vectors they
 
 )Qu8mg5v7";
 npe_function(morton_subtract)
-npe_arg(codes_1, dense_uint, dense_ulong, dense_ulonglong)
-npe_arg(codes_2, dense_uint, dense_ulong, dense_ulonglong)
+npe_arg(codes_1, dense_uint32, dense_uint64)
+npe_arg(codes_2, dense_uint32, dense_uint64)
 npe_default_arg(num_threads, int, -1)
 npe_doc(morton_subtract)
 npe_begin_code()
@@ -183,7 +183,7 @@ Encode n 3D points using Morton coding, possibly sorting them
 
 )Qu8mg5v7";
 npe_function(morton_encode)
-npe_arg(pts, dense_int, dense_long, dense_longlong)
+npe_arg(pts, dense_int32, dense_int64)
 npe_default_arg(num_threads, int, -1)
 npe_doc(morton_encode)
 npe_begin_code()
@@ -251,7 +251,7 @@ Decode n points along a Morton curve into 3D points
 
 )Qu8mg5v7";
 npe_function(morton_decode)
-npe_arg(codes, dense_uint, dense_ulong, dense_ulonglong)
+npe_arg(codes, dense_uint32, dense_uint64)
 npe_doc(morton_decode)
 npe_default_arg(num_threads, int, -1)
 npe_begin_code()
@@ -322,7 +322,7 @@ Queries a sorted array of morton encoded points to find the (approximate) k near
 
 )Qu8mg5v7";
 npe_function(morton_knn)
-npe_arg(codes, dense_uint, dense_ulong, dense_ulonglong)
+npe_arg(codes, dense_uint32, dense_uint64)
 npe_arg(qcodes, npe_matches(codes))
 npe_arg(k, int)
 npe_default_arg(sort_dist, bool, true)

diff --git a/src/orient_mesh_faces.cpp b/src/orient_mesh_faces.cpp
@@ -20,7 +20,7 @@ Consistently orient faces of a mesh within each connected component
 )igl_Qu8mg5v7";
 npe_function(orient_mesh_faces)
 npe_doc(orient_mesh_faces_doc)
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_default_arg(weighting_type, std::string, std::string("uniform"))
 npe_begin_code()
 {

diff --git a/src/point_areas.cpp b/src/point_areas.cpp
@@ -15,7 +15,7 @@ at a set of query points
 )igl_Qu8mg5v7";
 npe_function(estimate_point_cloud_areas)
 npe_arg(p, dense_float, dense_double)
-npe_arg(i, dense_int, dense_long, dense_longlong)
+npe_arg(i, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(n, npe_matches(v))
 npe_doc(estimate_point_cloud_areas_doc)
 npe_begin_code()

diff --git a/src/ray_mesh_intersection.cpp b/src/ray_mesh_intersection.cpp
@@ -18,7 +18,7 @@ void hack_extra_ray_mesh_bindings(pybind11::module& m) {
 
 npe_function(_populate_ray_intersector_internal)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(isector, std::shared_ptr<igl::embree::EmbreeIntersector>)
 npe_begin_code()
     igl::embree::EmbreeIntersector::PointMatrixType v_copy = v.template cast<float>();
@@ -106,7 +106,7 @@ Compute intersection between a set of rays and a triangle mesh
 )Qu8mg5v7";
 npe_function(ray_mesh_intersection)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(ray_o, npe_matches(v))
 npe_arg(ray_d, npe_matches(v))
 npe_default_arg(ray_near, double, 0.0)

diff --git a/src/remove_duplicates.cpp b/src/remove_duplicates.cpp
@@ -69,7 +69,7 @@ See also:
 npe_function(deduplicate_mesh_vertices)
 npe_doc(remove_duplicate_mesh_vertices_doc)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(epsilon, double)
 npe_default_arg(return_index, bool, true)
 npe_begin_code()

diff --git a/src/remove_unreferenced_mesh_vertices.cpp b/src/remove_unreferenced_mesh_vertices.cpp
@@ -23,7 +23,7 @@ some threshold
 npe_function(remove_unreferenced_mesh_vertices)
 npe_doc(remove_unreferenced_mesh_vertices_doc)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_begin_code()
 {
     validate_mesh(v, f);

diff --git a/src/sample_mesh.cpp b/src/sample_mesh.cpp
@@ -126,7 +126,7 @@ Downsample a point set (possibly on a mesh) so that samples are approximately ev
 )Qu8mg5v7";
 npe_function(sample_mesh_poisson_disk)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(num_samples, int)
 npe_default_arg(radius, double, 0.0)
 npe_default_arg(use_geodesic_distance, bool, true)
@@ -231,7 +231,7 @@ Generate uniformly distributed random point samples on a mesh
 )Qu8mg5v7";
 npe_function(sample_mesh_random)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(num_samples, int)
 npe_default_arg(random_seed, unsigned int, 0)
 npe_doc(sample_mesh_random_doc)

diff --git a/src/signed_distance.cpp b/src/signed_distance.cpp
@@ -22,7 +22,7 @@ Computes signed distances of a point cloud with respect to a Mesh using Fast Win
 npe_function(signed_distance_to_mesh)
 npe_arg(p, dense_float, dense_double)
 npe_arg(v, npe_matches(p))
-npe_arg(f, dense_int, dense_long, dense_longlong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_default_arg(lower_bound, float, -std::numeric_limits<float>::infinity())
 npe_default_arg(upper_bound, float, std::numeric_limits<float>::infinity())
 npe_doc(signed_distance_doc)

diff --git a/src/smooth.cpp b/src/smooth.cpp
@@ -41,7 +41,7 @@ Smooth a mesh using Laplacian smoothing
 npe_function(laplacian_smooth_mesh)
 npe_doc(laplacian_smooth_mesh_doc)
 npe_arg(v, dense_float, dense_double)
-npe_arg(f, dense_int, dense_longlong, dense_uint, dense_ulonglong)
+npe_arg(f, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(num_iters, int)
 npe_default_arg(use_cotan_weights, bool, false)
 npe_begin_code()

diff --git a/src/sparse_voxel_grid.cpp b/src/sparse_voxel_grid.cpp
@@ -159,7 +159,7 @@ npe_end_code()
 
 
 npe_function(dilate_sparse_voxel_grid_internal)
-npe_arg(grid_coordinates, dense_int, dense_long, dense_longlong)
+npe_arg(grid_coordinates, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_begin_code()
 {
     validate_sparse_voxel_grid(grid_coordinates);
@@ -244,7 +244,7 @@ npe_end_code()
 
 
 npe_function(erode_sparse_voxel_grid_internal)
-npe_arg(grid_coordinates, dense_int, dense_long, dense_longlong)
+npe_arg(grid_coordinates, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_begin_code()
 {
     validate_sparse_voxel_grid(grid_coordinates);
@@ -327,7 +327,7 @@ npe_end_code()
 
 
 npe_function(subdivide_sparse_voxel_grid_internal)
-npe_arg(grid_coordinates, dense_int, dense_long, dense_longlong)
+npe_arg(grid_coordinates, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_begin_code()
 {
     validate_sparse_voxel_grid(grid_coordinates);
@@ -383,7 +383,7 @@ npe_end_code()
 
 
 npe_function(sparse_voxel_grid_to_hex_mesh_internal)
-npe_arg(grid_coordinates, dense_int, dense_long, dense_longlong)
+npe_arg(grid_coordinates, dense_int32, dense_int64, dense_uint32, dense_uint64)
 npe_arg(gx, double)  // voxel size along x
 npe_arg(gy, double)  // voxel size along y
 npe_arg(gz, double)  // voxel size along z
@@ -471,7 +471,7 @@ Find the indices of the voxels which lie on the boundary of a sparse voxel grid
 
 )Qu8mg5v7";
 npe_function(sparse_voxel_grid_boundary)
-npe_arg(grid_coordinates, dense_int, dense_long, dense_longlong)
+npe_arg(grid_coordinates, dense_int32, dense_int64, dense_uint32, dense_uint64)
 // npe_doc(sparse_voxel_grid_boundary_doc)
 npe_begin_code()
 {