CGAL 6.1 - 3D Isosurfacing

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Isosurfacing_3/contouring_vtk_image.cpp
#include <CGAL/Simple_cartesian.h>
#include <CGAL/Isosurfacing_3/Cartesian_grid_3.h>
#include <CGAL/Isosurfacing_3/dual_contouring_3.h>
#include <CGAL/Isosurfacing_3/Dual_contouring_domain_3.h>
#include <CGAL/Isosurfacing_3/Finite_difference_gradient_3.h>
#include <CGAL/Isosurfacing_3/Interpolated_discrete_values_3.h>
#include <CGAL/Isosurfacing_3/marching_cubes_3.h>
#include <CGAL/Isosurfacing_3/Marching_cubes_domain_3.h>
#include <CGAL/Image_3.h>
#include <CGAL/IO/read_vtk_image_data.h>
#include <CGAL/Isosurfacing_3/IO/Image_3.h>
#include <CGAL/IO/polygon_soup_io.h>
#include <vtkNew.h>
#include <vtkImageData.h>
#include <vtkMetaImageReader.h>
#include <vtkXMLImageDataReader.h>
#include <vtkTIFFReader.h>
#include <vtkNrrdReader.h>
#include <vtkMINCImageReader.h>
#include <iostream>
#include <vector>
using Kernel = CGAL::Simple_cartesian<double>;
using FT = typename Kernel::FT;
using Point = typename Kernel::Point_3;
using Grid = CGAL::Isosurfacing::Cartesian_grid_3<Kernel>;
using Values = CGAL::Isosurfacing::Interpolated_discrete_values_3<Grid>;
using Gradients = CGAL::Isosurfacing::Finite_difference_gradient_3<Kernel>;
using Point_range = std::vector<Point>;
using Polygon_range = std::vector<std::vector<std::size_t> >;
namespace IS = CGAL::Isosurfacing;
void run_marching_cubes(const Grid& grid,
const FT isovalue,
const Values& values)
{
using Domain = IS::Marching_cubes_domain_3<Grid, Values, IS::Linear_interpolation_edge_intersection>;
std::cout << "\n ---- " << std::endl;
std::cout << "Running Marching Cubes with isovalue = " << isovalue << std::endl;
// fill up values
// create a domain from the grid
Domain domain { grid, values };
// prepare collections for the output indexed soup
Point_range points;
Polygon_range triangles;
// execute marching cubes
IS::marching_cubes<CGAL::Parallel_if_available_tag>(domain, isovalue, points, triangles);
std::cout << "Output #vertices: " << points.size() << std::endl;
std::cout << "Output #triangles: " << triangles.size() << std::endl;
// save output indexed mesh to a file, in the OFF format
CGAL::IO::write_polygon_soup("marching_cubes_vtk_image.off", points, triangles);
}
void run_dual_contouring(const Grid& grid,
const FT isovalue,
const Values& values)
{
using Domain = IS::Dual_contouring_domain_3<Grid, Values, Gradients, IS::Linear_interpolation_edge_intersection>;
std::cout << "\n ---- " << std::endl;
std::cout << "Running Dual Contouring with isovalue = " << isovalue << std::endl;
// fill up values and gradients
const FT step = CGAL::approximate_sqrt(grid.spacing().squared_length()) * 0.01; // finite difference step
Gradients gradients { values, step };
Domain domain { grid, values, gradients };
Point_range points;
Polygon_range triangles;
// run dual contouring isosurfacing
IS::dual_contouring<CGAL::Parallel_if_available_tag>(domain, isovalue, points, triangles);
std::cout << "Output #vertices: " << points.size() << std::endl;
std::cout << "Output #triangles: " << triangles.size() << std::endl;
CGAL::IO::write_polygon_soup("dual_contouring_vtk_image.off", points, triangles);
}
template <typename VtkReader>
void run(const char* filename,
const FT isovalue)
{
vtkNew<VtkReader> reader;
reader->SetFileName(filename);
reader->Update();
CGAL::Image_3 image = CGAL::IO::read_vtk_image_data(reader->GetOutput());
// convert image to a Cartesian grid
Grid grid;
Values values { grid }; // 'values' keeps a reference to the grid
if(!IS::IO::convert_image_to_grid(image, grid, values))
{
std::cerr << "Error: Cannot convert image to Cartesian grid" << std::endl;
return;
}
std::cout << "Span: " << grid.span() << std::endl;
std::cout << "Cell dimensions: " << grid.spacing()[0] << " " << grid.spacing()[1] << " " << grid.spacing()[2] << std::endl;
std::cout << "Cell #: " << grid.xdim() << ", " << grid.ydim() << ", " << grid.zdim() << std::endl;
run_marching_cubes(grid, isovalue, values);
run_dual_contouring(grid, isovalue, values);
}
int main(int argc, char* argv[])
{
const std::string fname = (argc>1) ? argv[1] : CGAL::data_file_path("images/torus_gray_image.vti");
const char* filename = fname.c_str();
const FT isovalue = (argc > 2) ? std::stod(argv[2]) : 3;
const std::string ext = CGAL::IO::internal::get_file_extension(filename);
if(ext == "mhd" || ext == "mha")
run<vtkMetaImageReader>(filename, isovalue);
else if(ext == "vti")
run<vtkXMLImageDataReader>(filename, isovalue);
else if(ext == "tif")
run<vtkTIFFReader>(filename, isovalue);
else if(ext == "nrrd")
run<vtkNrrdReader>(filename, isovalue);
else if(ext == "mnc")
run<vtkMINCImageReader>(filename, isovalue);
else
{
std::cerr << "Error: Unsupported file format" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
CGAL::Image_3
CGAL::Isosurfacing::Cartesian_grid_3
The class Cartesian_grid_3 represents a 3D Cartesian grid, that is the partition of an iso-cuboid int...
Definition: Cartesian_grid_3.h:148
CGAL::Isosurfacing::Finite_difference_gradient_3
Class template for a gradient that is calculated using finite differences.
Definition: Finite_difference_gradient_3.h:39
CGAL::Isosurfacing::Interpolated_discrete_values_3
Class template for a field of values that are calculated using discrete values and interpolation.
Definition: Interpolated_discrete_values_3.h:41
Kernel::Point_3
CGAL::IO::write_polygon_soup
bool write_polygon_soup(const std::string &fname, const PointRange &points, const PolygonRange &polygons, const NamedParameters &np=parameters::default_values())
CGAL::Isosurfacing
Definition: partition_traits.h:2
Kernel
CGAL::Simple_cartesian