Merge pull request #100 from nschloe/random-seed

Random seed

Author: nschloe

README.md

@@ -58,11 +58,12 @@ mesh = pygalmesh.generate_mesh(s, cell_size=0.2)
 
 # mesh.points, mesh.cells, ...
 ```
-You can write the mesh using [meshio](https://github.com/nschloe/meshio), e.g.,
+You can write the mesh with
 ```python
-import meshio
-meshio.write("out.vtk", mesh)
+mesh.write("out.vtk")
 ```
+You can use any format supported by [meshio](https://github.com/nschloe/meshio).
+
 The mesh generation comes with many more options, described
 [here](https://doc.cgal.org/latest/Mesh_3/). Try, for example,
 ```python
@@ -367,7 +368,7 @@ vol = vol.reshape((Nx,Ny,Nz))
 
 
 mesh = pygalmesh.generate_from_array(vol, h, facet_distance=.2, cell_size=1.)
-meshio.write('breast.vtk',mesh)
+mesh.write('breast.vtk')
 ```
 
 In addition, we can specify different mesh sizes for each tissue type. The code below sets the mesh size to  *1 mm* for the skin tissue (label `4`), *0.5 mm* for the vascular tissue (label `5`), and *2 mm* for all other tissues (`default`).
@@ -376,7 +377,7 @@ In addition, we can specify different mesh sizes for each tissue type. The code
 cell_sizes_map = {'default': 2., 4: 1., 5: .5}
 mesh = pygalmesh.generate_from_array_with_subdomain_sizing(
            vol, h, facet_distance=.2, cell_sizes_map=cell_sizes_map)
-meshio.write('breast_adapted.vtk',mesh)
+mesh.write('breast_adapted.vtk')
 ```
 
 #### Surface remeshing

pygalmesh/main.py

@@ -1,7 +1,6 @@
 import os
 import tempfile
 
-import meshio
 from _pygalmesh import (
     _generate_from_inr,
     _generate_from_inr_with_subdomain_sizing,
@@ -13,6 +12,8 @@
     _remesh_surface,
 )
 
+import meshio
+
 
 def generate_mesh(
     domain,
@@ -29,6 +30,7 @@ def generate_mesh(
     cell_radius_edge_ratio=0.0,
     cell_size=0.0,
     verbose=True,
+    seed=0,
 ):
     feature_edges = [] if feature_edges is None else feature_edges
 
@@ -51,6 +53,7 @@ def generate_mesh(
         cell_radius_edge_ratio=cell_radius_edge_ratio,
         cell_size=cell_size,
         verbose=verbose,
+        seed=seed,
     )
 
     mesh = meshio.read(outfile)
@@ -73,6 +76,7 @@ def generate_with_sizing_field(
     cell_radius_edge_ratio=0.0,
     cell_size=None,
     verbose=True,
+    seed=0,
 ):
     feature_edges = [] if feature_edges is None else feature_edges
 
@@ -95,6 +99,7 @@ def generate_with_sizing_field(
         cell_radius_edge_ratio=cell_radius_edge_ratio,
         cell_size=cell_size,
         verbose=verbose,
+        seed=seed,
     )
 
     mesh = meshio.read(outfile)
@@ -117,6 +122,7 @@ def generate_periodic_mesh(
     cell_size=0.0,
     number_of_copies_in_output=1,
     verbose=True,
+    seed=0,
 ):
     fh, outfile = tempfile.mkstemp(suffix=".mesh")
     os.close(fh)
@@ -139,6 +145,7 @@ def generate_periodic_mesh(
         cell_size=cell_size,
         number_of_copies_in_output=number_of_copies_in_output,
         verbose=verbose,
+        seed=seed,
     )
 
     mesh = meshio.read(outfile)
@@ -153,6 +160,7 @@ def generate_surface_mesh(
     radius_bound=0.0,
     distance_bound=0.0,
     verbose=True,
+    seed=0,
 ):
     fh, outfile = tempfile.mkstemp(suffix=".off")
     os.close(fh)
@@ -165,6 +173,7 @@ def generate_surface_mesh(
         radius_bound=radius_bound,
         distance_bound=distance_bound,
         verbose=verbose,
+        seed=seed,
     )
 
     mesh = meshio.read(outfile)
@@ -185,6 +194,7 @@ def generate_volume_mesh_from_surface_mesh(
     cell_radius_edge_ratio=0.0,
     cell_size=0.0,
     verbose=True,
+    seed=0,
 ):
     mesh = meshio.read(filename)
 
@@ -209,6 +219,7 @@ def generate_volume_mesh_from_surface_mesh(
         cell_radius_edge_ratio=cell_radius_edge_ratio,
         cell_size=cell_size,
         verbose=verbose,
+        seed=seed,
     )
 
     mesh = meshio.read(outfile)
@@ -230,6 +241,7 @@ def generate_from_inr(
     cell_radius_edge_ratio=0.0,
     cell_size=0.0,
     verbose=True,
+    seed=0,
 ):
     fh, outfile = tempfile.mkstemp(suffix=".mesh")
     os.close(fh)
@@ -248,6 +260,7 @@ def generate_from_inr(
         cell_radius_edge_ratio=cell_radius_edge_ratio,
         cell_size=cell_size,
         verbose=verbose,
+        seed=seed,
     )
 
     mesh = meshio.read(outfile)
@@ -268,6 +281,7 @@ def generate_from_inr_with_subdomain_sizing(
     facet_distance=0.0,
     cell_radius_edge_ratio=0.0,
     verbose=True,
+    seed=0,
 ):
     fh, outfile = tempfile.mkstemp(suffix=".mesh")
     os.close(fh)
@@ -296,6 +310,7 @@ def generate_from_inr_with_subdomain_sizing(
         facet_distance=facet_distance,
         cell_radius_edge_ratio=cell_radius_edge_ratio,
         verbose=verbose,
+        seed=seed,
     )
 
     mesh = meshio.read(outfile)
@@ -310,6 +325,7 @@ def remesh_surface(
     facet_size=0.0,
     facet_distance=0.0,
     verbose=True,
+    seed=0,
 ):
     mesh = meshio.read(filename)
 
@@ -328,6 +344,7 @@ def remesh_surface(
         facet_size=facet_size,
         facet_distance=facet_distance,
         verbose=verbose,
+        seed=seed,
     )
 
     mesh = meshio.read(outfile)
@@ -425,6 +442,7 @@ def generate_from_array_with_subdomain_sizing(
     facet_distance=0.0,
     cell_radius_edge_ratio=0.0,
     verbose=True,
+    seed=0,
 ):
     assert vol.dtype in ["uint8", "uint16"]
     fh, inr_filename = tempfile.mkstemp(suffix=".inr")
@@ -443,6 +461,7 @@ def generate_from_array_with_subdomain_sizing(
         facet_distance,
         cell_radius_edge_ratio,
         verbose,
+        seed,
     )
     os.remove(inr_filename)
     return mesh

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pygalmesh
-version = 0.6.6
+version = 0.6.7
 url = https://github.com/nschloe/pygalmesh
 author = Nico Schlömer
 email = nico.schloemer@gmail.com
@@ -27,7 +27,7 @@ classifiers =
 packages = find:
 setup_requires = pybind11 >= 2.2
 install_requires =
-    importlib_metadata
+    importlib_metadata;python_version<"3.8"
     meshio >= 4.0.0, < 5.0.0
     numpy
     pybind11 >= 2.2

src/generate.cpp

@@ -60,9 +60,12 @@ generate_mesh(
     const double facet_distance,
     const double cell_radius_edge_ratio,
     const double cell_size,
-    const bool verbose
+    const bool verbose,
+    const int seed
     )
 {
+  CGAL::get_default_random() = CGAL::Random(seed);
+
   const double bounding_sphere_radius2 = bounding_sphere_radius > 0 ?
     bounding_sphere_radius*bounding_sphere_radius :
     // some wiggle room
@@ -134,9 +137,12 @@ generate_with_sizing_field(
     const double facet_distance,
     const double cell_radius_edge_ratio,
     const std::shared_ptr<pygalmesh::SizingFieldBase> & cell_size,
-    const bool verbose
+    const bool verbose,
+    const int seed
     )
 {
+  CGAL::get_default_random() = CGAL::Random(seed);
+
   const double bounding_sphere_radius2 = bounding_sphere_radius > 0 ?
     bounding_sphere_radius*bounding_sphere_radius :
     // some wiggle room

src/generate.hpp

@@ -25,7 +25,8 @@ void generate_mesh(
     const double facet_distance = 0.0,
     const double cell_radius_edge_ratio = 0.0,
     const double cell_size = 0.0,
-    const bool verbose = true
+    const bool verbose = true,
+    const int seed = 0
     );
 
 void generate_with_sizing_field(
@@ -43,7 +44,8 @@ void generate_with_sizing_field(
     const double facet_distance = 0.0,
     const double cell_radius_edge_ratio = 0.0,
     const std::shared_ptr<pygalmesh::SizingFieldBase> & cell_size = nullptr,
-    const bool verbose = true
+    const bool verbose = true,
+    const int seed = 0
     );
 
 } // namespace pygalmesh

src/generate_from_inr.cpp

@@ -47,9 +47,12 @@ generate_from_inr(
     const double facet_distance,
     const double cell_radius_edge_ratio,
     const double cell_size,
-    const bool verbose
+    const bool verbose,
+    const int seed
     )
 {
+  CGAL::get_default_random() = CGAL::Random(seed);
+
   CGAL::Image_3 image;
   const bool success = image.read(inr_filename.c_str());
   if (!success) {
@@ -95,9 +98,9 @@ void
 generate_from_inr_with_subdomain_sizing(
     const std::string & inr_filename,
     const std::string & outfile,
-	const double default_cell_size,
+    const double default_cell_size,
     const std::vector<double> & cell_sizes,
-	const std::vector<int> & cell_labels,
+    const std::vector<int> & cell_labels,
     const bool lloyd,
     const bool odt,
     const bool perturb,
@@ -107,9 +110,12 @@ generate_from_inr_with_subdomain_sizing(
     const double facet_size,
     const double facet_distance,
     const double cell_radius_edge_ratio,
-    const bool verbose
+    const bool verbose,
+    const int seed
     )
 {
+  CGAL::get_default_random() = CGAL::Random(seed);
+
   CGAL::Image_3 image;
   const bool success = image.read(inr_filename.c_str());
   if (!success) {
@@ -120,7 +126,7 @@ generate_from_inr_with_subdomain_sizing(
   Sizing_field_cell cell_size(default_cell_size);
   const int ndimensions = 3;
   for(std::vector<double>::size_type i(0); i < cell_sizes.size(); ++i)
-	  cell_size.set_size(cell_sizes[i], ndimensions, cgal_domain.index_from_subdomain_index(cell_labels[i]));
+    cell_size.set_size(cell_sizes[i], ndimensions, cgal_domain.index_from_subdomain_index(cell_labels[i]));
 
   Mesh_criteria criteria(
       CGAL::parameters::edge_size=edge_size,

src/generate_from_inr.hpp

@@ -19,16 +19,17 @@ void generate_from_inr(
     const double facet_distance = 0.0,
     const double cell_radius_edge_ratio = 0.0,
     const double cell_size = 0.0,
-    const bool verbose = true
+    const bool verbose = true,
+    const int seed = 0
     );
 
 void
 generate_from_inr_with_subdomain_sizing(
     const std::string & inr_filename,
     const std::string & outfile,
-	const double default_cell_size,
+    const double default_cell_size,
     const std::vector<double> & cell_sizes,
-	const std::vector<int> & cell_labels,
+    const std::vector<int> & cell_labels,
     const bool lloyd = false,
     const bool odt = false,
     const bool perturb  = true,
@@ -38,7 +39,8 @@ generate_from_inr_with_subdomain_sizing(
     const double facet_size = 0.0,
     const double facet_distance = 0.0,
     const double cell_radius_edge_ratio = 0.0,
-    const bool verbose  = true
+    const bool verbose  = true,
+    const int seed = 0
     );
 
 } // namespace pygalmesh

src/generate_from_off.cpp

@@ -29,13 +29,24 @@ typedef CGAL::Mesh_criteria_3<Tr> Mesh_criteria;
 // To avoid verbose function and named parameters call
 using namespace CGAL::parameters;
 
-void generate_from_off(const std::string& infile, const std::string& outfile,
-                       const bool lloyd, const bool odt, const bool perturb,
-                       const bool exude, const double edge_size,
-                       const double facet_angle, const double facet_size,
-                       const double facet_distance,
-                       const double cell_radius_edge_ratio,
-                       const double cell_size, const bool verbose) {
+void generate_from_off(
+    const std::string& infile,
+    const std::string& outfile,
+    const bool lloyd,
+    const bool odt,
+    const bool perturb,
+    const bool exude,
+    const double edge_size,
+    const double facet_angle,
+    const double facet_size,
+    const double facet_distance,
+    const double cell_radius_edge_ratio,
+    const double cell_size,
+    const bool verbose,
+    const int seed
+) {
+  CGAL::get_default_random() = CGAL::Random(seed);
+
   // Create input polyhedron
   Polyhedron polyhedron;
   std::ifstream input(infile);

src/generate_from_off.hpp

@@ -20,7 +20,8 @@ generate_from_off(
     const double facet_distance = 0.0,
     const double cell_radius_edge_ratio = 0.0,
     const double cell_size = 0.0,
-    const bool verbose = true
+    const bool verbose = true,
+    const int seed = 0
     );
 
 } // namespace pygalmesh

src/generate_periodic.cpp

@@ -64,9 +64,12 @@ generate_periodic_mesh(
     const double cell_radius_edge_ratio,
     const double cell_size,
     const int number_of_copies_in_output,
-    const bool verbose
+    const bool verbose,
+    const int seed
     )
 {
+  CGAL::get_default_random() = CGAL::Random(seed);
+
   K::Iso_cuboid_3 cuboid(
       bounding_cuboid[0],
       bounding_cuboid[1],