diff --git a/Mesh_3/doc/Mesh_3/Mesh_3.txt b/Mesh_3/doc/Mesh_3/Mesh_3.txt index 86a2dd81e38..45503259386 100644 --- a/Mesh_3/doc/Mesh_3/Mesh_3.txt +++ b/Mesh_3/doc/Mesh_3/Mesh_3.txt @@ -573,13 +573,6 @@ constructor of the `Mesh_criteria` instance. Cut view of a 3D mesh produced from an implicit domain \cgalFigureEnd -\subsubsection Mesh_33DDomainsGrayImageIsosurfaces 3D Domains Bounded by Isosurfaces in 3D Gray-Level Images - -The following example produces a 3D mesh for a domain whose boundary surface -is the isosurface associated to an isovalue inside the input gray-level -3D image. In the distribution you can also find the example \ref Mesh_3/mesh_3D_gray_vtk_image.cpp which can deal with DICOM files as input. - -\cgalExample{Mesh_3/mesh_3D_gray_image.cpp} \subsection Mesh_3MeshingMultipleDomains Meshing Multiple Domains @@ -682,8 +675,18 @@ This allows to remesh a surface, and is equivalent to the function `make_surface View of a remeshed surface. (Left) input mesh (Right) output mesh. Code from subsection \ref Mesh_3RemeshingPolyhedralSurface generates the file. \cgalFigureEnd -\subsection Mesh_3DomainsFromSegmented3DImages Domains From Segmented 3D Images +\subsection Mesh_3DomainsFrom3DImages Domains From 3D Images +\subsubsection Mesh_33DDomainsGrayImageIsosurfaces 3D Domains Bounded by Isosurfaces in 3D Gray-Level Images + +The following example produces a 3D mesh for a domain whose boundary surface +is the isosurface associated to an isovalue inside the input gray-level +3D image. In the distribution you can also find the example \ref Mesh_3/mesh_3D_gray_vtk_image.cpp which can deal with DICOM files as input. + +\cgalExample{Mesh_3/mesh_3D_gray_image.cpp} + + +\subsubsection Mesh_3DomainsFromSegmented3DImages Domains From Segmented 3D Images \anchor Mesh_3_subsection_examples_3d_image The following code produces a 3D mesh from a 3D image. The image is a segmented medical image in which each @@ -703,7 +706,7 @@ The resulting mesh is shown in \cgalFigureRef{figureliver_3d_image_mesh}. Cut view of a 3D mesh produced from a segmented liver image. Code from subsection \ref Mesh_3_subsection_examples_3d_image generates this file. \cgalFigureEnd -\subsubsection Mesh_3DomainsFromSegmented3DImagesWithCustomInitialization Domains From Segmented 3D Images, with a Custom Initialization +\subsubsection Mesh_3DomainsFrom3DImagesWithCustomInitialization Domains From 3D Images, with a Custom Initialization The example \ref Mesh_3/mesh_3D_image_with_custom_initialization.cpp is a modification of \ref Mesh_3/mesh_3D_image.cpp. The goal of that example is to show how @@ -788,6 +791,25 @@ create a 3D image using the undocumented API of CGAL_ImageIO. The code of the function `%random_labeled_image()` is in the header file \ref Mesh_3/random_labeled_image.h\. + +The example \ref Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp is another +custom initialization example, for meshing of 3D gray-level images. Similarly to +the segmented image example above, the code consists in: + -# the creation of an empty `%c3t3` object, + -# a call to a non-documented function + `initialize_triangulation_from_gray_image()` that inserts points in + the triangulation, + -# then the call to `refine_mesh_3()`. + +\snippet Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp Meshing + +The code of the function `initialize_triangulation_from_gray_image()` is +in the non-documented header \ref +CGAL/Mesh_3/initialize_triangulation_from_gray_image.h\. As it is +undocumented and may be removed or modified at any time, if you wish to +use it then you should copy-paste it to your user code. + + \subsection Mesh_3UsingVariableSizingField Using Variable Sizing Field \subsubsection Mesh_3SizingFieldasanAnalyticalFunction Sizing Field as an Analytical Function diff --git a/Mesh_3/doc/Mesh_3/examples.txt b/Mesh_3/doc/Mesh_3/examples.txt index eaa86c94551..c1c5e4de1a8 100644 --- a/Mesh_3/doc/Mesh_3/examples.txt +++ b/Mesh_3/doc/Mesh_3/examples.txt @@ -1,9 +1,11 @@ /*! \example Mesh_3/implicit_functions.cpp \example Mesh_3/mesh_3D_image.cpp +\example Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp \example Mesh_3/mesh_3D_image_with_features.cpp \example Mesh_3/mesh_3D_image_with_custom_initialization.cpp \example Mesh_3/random_labeled_image.h +\example CGAL/Mesh_3/initialize_triangulation_from_gray_image.h \example CGAL/Mesh_3/initialize_triangulation_from_labeled_image.h \example Mesh_3/mesh_3D_image_variable_size.cpp \example Mesh_3/mesh_hybrid_mesh_domain.cpp diff --git a/Mesh_3/examples/Mesh_3/CMakeLists.txt b/Mesh_3/examples/Mesh_3/CMakeLists.txt index 2f9ba7d5b27..9bfe5fd85a0 100644 --- a/Mesh_3/examples/Mesh_3/CMakeLists.txt +++ b/Mesh_3/examples/Mesh_3/CMakeLists.txt @@ -149,6 +149,11 @@ if(TARGET CGAL::CGAL_ImageIO) target_link_libraries(mesh_3D_image_with_custom_initialization PUBLIC CGAL::Eigen3_support) + create_single_source_cgal_program( + "mesh_3D_gray_image_with_custom_initialization.cpp") + target_link_libraries(mesh_3D_gray_image_with_custom_initialization + PUBLIC CGAL::Eigen3_support) + create_single_source_cgal_program("mesh_3D_image_variable_size.cpp") target_link_libraries(mesh_3D_image_variable_size PUBLIC CGAL::Eigen3_support) @@ -172,6 +177,7 @@ if(CGAL_ACTIVATE_CONCURRENT_MESH_3 AND TARGET CGAL::TBB_support) mesh_3D_image mesh_3D_image_variable_size mesh_3D_image_with_custom_initialization + mesh_3D_gray_image_with_custom_initialization mesh_3D_image_with_features mesh_implicit_domains mesh_implicit_sphere diff --git a/Mesh_3/examples/Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp b/Mesh_3/examples/Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp new file mode 100644 index 00000000000..533637a3f75 --- /dev/null +++ b/Mesh_3/examples/Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp @@ -0,0 +1,71 @@ + +#include + +#include +#include +#include + +#include + +#include +#include +#include +#include + +typedef float Image_word_type; + +// Domain +typedef CGAL::Exact_predicates_inexact_constructions_kernel K; +typedef CGAL::Labeled_mesh_domain_3 Mesh_domain; + +// Parallel tag +#ifdef CGAL_CONCURRENT_MESH_3 +typedef CGAL::Parallel_tag Concurrency_tag; +#else +typedef CGAL::Sequential_tag Concurrency_tag; +#endif + +// Triangulation +typedef CGAL::Mesh_triangulation_3::type Tr; +typedef CGAL::Mesh_complex_3_in_triangulation_3 C3t3; + +// Criteria +typedef CGAL::Mesh_criteria_3 Mesh_criteria; + +// To avoid verbose function and named parameters call +using namespace CGAL::parameters; + +int main(int argc, char* argv[]) +{ + const char* fname = (argc > 1) ? argv[1] : "data/skull_2.9.inr"; + /// [Load image] + CGAL::Image_3 image; + if (!image.read(fname)) { + std::cerr << "Error: Cannot read file " << fname << std::endl; + return EXIT_FAILURE; + } + /// [Domain creation] + Mesh_domain domain = + Mesh_domain::create_gray_image_mesh_domain(image, 2.9f, 0.f); + /// [Domain creation] + + /// [Mesh criteria] + Mesh_criteria criteria(facet_angle = 30, facet_size = 6, facet_distance = 2, + cell_radius_edge_ratio = 3, cell_size = 8); + + /// [Meshing] + C3t3 c3t3; + initialize_triangulation_from_gray_image(c3t3, + domain, + image, + criteria, + 2.9f,//isolevel + Image_word_type(0)); + CGAL::refine_mesh_3(c3t3, domain, criteria); + /// [Meshing] + + /// Output + CGAL::dump_c3t3(c3t3, "out"); + + return 0; +} diff --git a/Mesh_3/include/CGAL/Mesh_3/initialize_triangulation_from_gray_image.h b/Mesh_3/include/CGAL/Mesh_3/initialize_triangulation_from_gray_image.h new file mode 100644 index 00000000000..1d3a6b7601e --- /dev/null +++ b/Mesh_3/include/CGAL/Mesh_3/initialize_triangulation_from_gray_image.h @@ -0,0 +1,50 @@ +// Copyright (c) 2015,2016 GeometryFactory +// All rights reserved. +// +// This file is part of CGAL (www.cgal.org). +// +// $URL$ +// $Id$ +// SPDX-License-Identifier: GPL-3.0-or-later OR LicenseRef-Commercial +// +// +// Author(s) : Laurent Rineau, Jane Tournois + +#ifndef CGAL_MESH_3_INITIALIZE_TRIANGULATION_FROM_GRAY_IMAGE_H +#define CGAL_MESH_3_INITIALIZE_TRIANGULATION_FROM_GRAY_IMAGE_H + +#include + +#include +#include + +#include + +template +void initialize_triangulation_from_gray_image(C3T3& c3t3, + const MeshDomain& domain, + const CGAL::Image_3& image, + const MeshCriteria& criteria, + const FT& iso_value, + Image_word_type, + const Functor image_values_to_subdomain_indices = CGAL::Null_functor(), + bool protect_features = false) +{ + typedef typename CGAL::Default::Get::type Functor_; + + using CGAL::Mesh_3::internal::Create_gray_image_values_to_subdomain_indices; + typedef Create_gray_image_values_to_subdomain_indices C_i_v_t_s_i; + typedef typename C_i_v_t_s_i::type Image_values_to_subdomain_indices; + Image_values_to_subdomain_indices transform_fct = + C_i_v_t_s_i()(image_values_to_subdomain_indices, iso_value); + + initialize_triangulation_from_labeled_image(c3t3, domain, image, criteria, + Image_word_type(), + protect_features, + transform_fct); +} + +#endif // CGAL_MESH_3_INITIALIZE_TRIANGULATION_FROM_GRAY_IMAGE_H diff --git a/Mesh_3/include/CGAL/Mesh_3/initialize_triangulation_from_labeled_image.h b/Mesh_3/include/CGAL/Mesh_3/initialize_triangulation_from_labeled_image.h index 873ae27786a..571a4171e5d 100644 --- a/Mesh_3/include/CGAL/Mesh_3/initialize_triangulation_from_labeled_image.h +++ b/Mesh_3/include/CGAL/Mesh_3/initialize_triangulation_from_labeled_image.h @@ -17,6 +17,7 @@ #include #include +#include #include #include @@ -31,17 +32,23 @@ template struct Get_point { const double vx, vy, vz; + const double tx, ty, tz; Get_point(const CGAL::Image_3* image) : vx(image->vx()) , vy(image->vy()) , vz(image->vz()) + , tx(image->tx()) + , ty(image->ty()) + , tz(image->tz()) {} Point operator()(const std::size_t i, const std::size_t j, const std::size_t k) const { - return Point(double(i) * vx, double(j) * vy, double(k) * vz); + return Point(double(i) * vx + tx, + double(j) * vy + ty, + double(k) * vz + tz); } }; template @@ -64,16 +71,16 @@ void init_tr_from_labeled_image_call_init_features(C3T3& c3t3, << " initial points on 1D-features" << std::endl; } - template + typename Image_word_type, + typename TransformOperator = CGAL::Identity > void initialize_triangulation_from_labeled_image(C3T3& c3t3, - const MeshDomain& domain, - const CGAL::Image_3& image, - const MeshCriteria& criteria, - Image_word_type, - bool protect_features = false - ) + const MeshDomain& domain, + const CGAL::Image_3& image, + const MeshCriteria& criteria, + Image_word_type, + bool protect_features = false, + TransformOperator transform = CGAL::Identity()) { typedef typename C3T3::Triangulation Tr; typedef typename Tr::Geom_traits Gt; @@ -111,11 +118,10 @@ void initialize_triangulation_from_labeled_image(C3T3& c3t3, Seeds seeds; Get_point get_point(&image); std::cout << "Searching for connected components..." << std::endl; - CGAL::Identity no_transformation; search_for_connected_components_in_labeled_image(image, std::back_inserter(seeds), CGAL::Emptyset_iterator(), - no_transformation, + transform, get_point, Image_word_type()); std::cout << " " << seeds.size() << " components were found." << std::endl;