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Merge pull request #5463 from janetournois/Mesh_3-example_initialization_cc_in_gray_images-jtournois
Mesh 3 - connected components initialization for 3D gray images
This commit is contained in:
Laurent Rineau
commit
0cb823656a
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@ -573,13 +573,6 @@ constructor of the `Mesh_criteria` instance.
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Cut view of a 3D mesh produced from an implicit domain
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\cgalFigureEnd
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\subsubsection Mesh_33DDomainsGrayImageIsosurfaces 3D Domains Bounded by Isosurfaces in 3D Gray-Level Images
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The following example produces a 3D mesh for a domain whose boundary surface
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is the isosurface associated to an isovalue inside the input gray-level
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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.
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\cgalExample{Mesh_3/mesh_3D_gray_image.cpp}
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\subsection Mesh_3MeshingMultipleDomains Meshing Multiple Domains
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@ -682,8 +675,18 @@ This allows to remesh a surface, and is equivalent to the function `make_surface
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View of a remeshed surface. (Left) input mesh (Right) output mesh. Code from subsection \ref Mesh_3RemeshingPolyhedralSurface generates the file.
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\cgalFigureEnd
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\subsection Mesh_3DomainsFromSegmented3DImages Domains From Segmented 3D Images
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\subsection Mesh_3DomainsFrom3DImages Domains From 3D Images
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\subsubsection Mesh_33DDomainsGrayImageIsosurfaces 3D Domains Bounded by Isosurfaces in 3D Gray-Level Images
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The following example produces a 3D mesh for a domain whose boundary surface
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is the isosurface associated to an isovalue inside the input gray-level
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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.
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\cgalExample{Mesh_3/mesh_3D_gray_image.cpp}
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\subsubsection Mesh_3DomainsFromSegmented3DImages Domains From Segmented 3D Images
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\anchor Mesh_3_subsection_examples_3d_image
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The following code produces a 3D mesh from
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a 3D image. The image is a segmented medical image in which each
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@ -703,7 +706,7 @@ The resulting mesh is shown in \cgalFigureRef{figureliver_3d_image_mesh}.
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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.
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\cgalFigureEnd
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\subsubsection Mesh_3DomainsFromSegmented3DImagesWithCustomInitialization Domains From Segmented 3D Images, with a Custom Initialization
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\subsubsection Mesh_3DomainsFrom3DImagesWithCustomInitialization Domains From 3D Images, with a Custom Initialization
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The example \ref Mesh_3/mesh_3D_image_with_custom_initialization.cpp is a modification
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of \ref Mesh_3/mesh_3D_image.cpp. The goal of that example is to show how
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@ -788,6 +791,25 @@ create a 3D image using the undocumented API of CGAL_ImageIO.
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The code of the function `%random_labeled_image()` is in the header file \ref
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Mesh_3/random_labeled_image.h\.
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The example \ref Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp is another
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custom initialization example, for meshing of 3D gray-level images. Similarly to
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the segmented image example above, the code consists in:
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-# the creation of an empty `%c3t3` object,
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-# a call to a non-documented function
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`initialize_triangulation_from_gray_image()` that inserts points in
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the triangulation,
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-# then the call to `refine_mesh_3()`.
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\snippet Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp Meshing
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The code of the function `initialize_triangulation_from_gray_image()` is
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in the non-documented header \ref
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CGAL/Mesh_3/initialize_triangulation_from_gray_image.h\. As it is
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undocumented and may be removed or modified at any time, if you wish to
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use it then you should copy-paste it to your user code.
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\subsection Mesh_3UsingVariableSizingField Using Variable Sizing Field
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\subsubsection Mesh_3SizingFieldasanAnalyticalFunction Sizing Field as an Analytical Function
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@ -1,9 +1,11 @@
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/*!
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\example Mesh_3/implicit_functions.cpp
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\example Mesh_3/mesh_3D_image.cpp
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\example Mesh_3/mesh_3D_gray_image_with_custom_initialization.cpp
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\example Mesh_3/mesh_3D_image_with_features.cpp
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\example Mesh_3/mesh_3D_image_with_custom_initialization.cpp
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\example Mesh_3/random_labeled_image.h
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\example CGAL/Mesh_3/initialize_triangulation_from_gray_image.h
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\example CGAL/Mesh_3/initialize_triangulation_from_labeled_image.h
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\example Mesh_3/mesh_3D_image_variable_size.cpp
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\example Mesh_3/mesh_hybrid_mesh_domain.cpp
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@ -149,6 +149,11 @@ if(TARGET CGAL::CGAL_ImageIO)
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target_link_libraries(mesh_3D_image_with_custom_initialization
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PUBLIC CGAL::Eigen3_support)
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create_single_source_cgal_program(
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"mesh_3D_gray_image_with_custom_initialization.cpp")
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target_link_libraries(mesh_3D_gray_image_with_custom_initialization
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PUBLIC CGAL::Eigen3_support)
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create_single_source_cgal_program("mesh_3D_image_variable_size.cpp")
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target_link_libraries(mesh_3D_image_variable_size
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PUBLIC CGAL::Eigen3_support)
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@ -172,6 +177,7 @@ if(CGAL_ACTIVATE_CONCURRENT_MESH_3 AND TARGET CGAL::TBB_support)
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mesh_3D_image
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mesh_3D_image_variable_size
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mesh_3D_image_with_custom_initialization
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mesh_3D_gray_image_with_custom_initialization
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mesh_3D_image_with_features
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mesh_implicit_domains
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mesh_implicit_sphere
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@ -0,0 +1,71 @@
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#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
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#include <CGAL/Mesh_triangulation_3.h>
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#include <CGAL/Mesh_complex_3_in_triangulation_3.h>
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#include <CGAL/Mesh_criteria_3.h>
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#include <CGAL/Mesh_3/initialize_triangulation_from_gray_image.h>
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#include <CGAL/Labeled_mesh_domain_3.h>
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#include <CGAL/make_mesh_3.h>
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#include <CGAL/Image_3.h>
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#include <functional>
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typedef float Image_word_type;
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// Domain
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typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
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typedef CGAL::Labeled_mesh_domain_3<K> Mesh_domain;
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// Parallel tag
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#ifdef CGAL_CONCURRENT_MESH_3
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typedef CGAL::Parallel_tag Concurrency_tag;
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#else
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typedef CGAL::Sequential_tag Concurrency_tag;
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#endif
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// Triangulation
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typedef CGAL::Mesh_triangulation_3<Mesh_domain, CGAL::Default, Concurrency_tag>::type Tr;
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typedef CGAL::Mesh_complex_3_in_triangulation_3<Tr> C3t3;
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// Criteria
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typedef CGAL::Mesh_criteria_3<Tr> Mesh_criteria;
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// To avoid verbose function and named parameters call
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using namespace CGAL::parameters;
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int main(int argc, char* argv[])
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{
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const char* fname = (argc > 1) ? argv[1] : "data/skull_2.9.inr";
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/// [Load image]
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CGAL::Image_3 image;
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if (!image.read(fname)) {
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std::cerr << "Error: Cannot read file " << fname << std::endl;
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return EXIT_FAILURE;
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}
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/// [Domain creation]
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Mesh_domain domain =
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Mesh_domain::create_gray_image_mesh_domain(image, 2.9f, 0.f);
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/// [Domain creation]
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/// [Mesh criteria]
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Mesh_criteria criteria(facet_angle = 30, facet_size = 6, facet_distance = 2,
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cell_radius_edge_ratio = 3, cell_size = 8);
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/// [Meshing]
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C3t3 c3t3;
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initialize_triangulation_from_gray_image(c3t3,
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domain,
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image,
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criteria,
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2.9f,//isolevel
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Image_word_type(0));
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CGAL::refine_mesh_3(c3t3, domain, criteria);
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/// [Meshing]
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/// Output
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CGAL::dump_c3t3(c3t3, "out");
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return 0;
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}
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@ -0,0 +1,50 @@
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// Copyright (c) 2015,2016 GeometryFactory
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// All rights reserved.
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//
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// This file is part of CGAL (www.cgal.org).
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//
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// $URL$
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// $Id$
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// SPDX-License-Identifier: GPL-3.0-or-later OR LicenseRef-Commercial
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//
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//
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// Author(s) : Laurent Rineau, Jane Tournois
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#ifndef CGAL_MESH_3_INITIALIZE_TRIANGULATION_FROM_GRAY_IMAGE_H
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#define CGAL_MESH_3_INITIALIZE_TRIANGULATION_FROM_GRAY_IMAGE_H
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#include <CGAL/license/Mesh_3.h>
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#include <CGAL/Labeled_mesh_domain_3.h>
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#include <CGAL/Mesh_3/initialize_triangulation_from_labeled_image.h>
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#include <CGAL/tags.h>
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template<class C3T3, class MeshDomain, class MeshCriteria,
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typename FT,
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typename Image_word_type,
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typename Functor = CGAL::Null_functor>
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void initialize_triangulation_from_gray_image(C3T3& c3t3,
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const MeshDomain& domain,
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const CGAL::Image_3& image,
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const MeshCriteria& criteria,
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const FT& iso_value,
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Image_word_type,
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const Functor image_values_to_subdomain_indices = CGAL::Null_functor(),
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bool protect_features = false)
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{
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typedef typename CGAL::Default::Get<Functor, CGAL::Null_functor>::type Functor_;
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using CGAL::Mesh_3::internal::Create_gray_image_values_to_subdomain_indices;
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typedef Create_gray_image_values_to_subdomain_indices<Functor_> C_i_v_t_s_i;
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typedef typename C_i_v_t_s_i::type Image_values_to_subdomain_indices;
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Image_values_to_subdomain_indices transform_fct =
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C_i_v_t_s_i()(image_values_to_subdomain_indices, iso_value);
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initialize_triangulation_from_labeled_image(c3t3, domain, image, criteria,
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Image_word_type(),
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protect_features,
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transform_fct);
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}
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#endif // CGAL_MESH_3_INITIALIZE_TRIANGULATION_FROM_GRAY_IMAGE_H
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@ -17,6 +17,7 @@
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#include <CGAL/Mesh_3/search_for_connected_components_in_labeled_image.h>
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#include <CGAL/Mesh_3/squared_distance_Point_3_Triangle_3.h>
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#include <CGAL/Labeled_mesh_domain_3.h>
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#include <CGAL/make_mesh_3.h>
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#include <CGAL/enum.h>
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@ -31,17 +32,23 @@ template <typename Point>
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struct Get_point
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{
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const double vx, vy, vz;
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const double tx, ty, tz;
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Get_point(const CGAL::Image_3* image)
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: vx(image->vx())
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, vy(image->vy())
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, vz(image->vz())
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, tx(image->tx())
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, ty(image->ty())
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, tz(image->tz())
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{}
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Point operator()(const std::size_t i,
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const std::size_t j,
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const std::size_t k) const
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{
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return Point(double(i) * vx, double(j) * vy, double(k) * vz);
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return Point(double(i) * vx + tx,
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double(j) * vy + ty,
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double(k) * vz + tz);
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}
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};
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template<class C3T3, class MeshDomain, class MeshCriteria>
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@ -64,16 +71,16 @@ void init_tr_from_labeled_image_call_init_features(C3T3& c3t3,
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<< " initial points on 1D-features" << std::endl;
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}
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template<class C3T3, class MeshDomain, class MeshCriteria,
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typename Image_word_type>
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typename Image_word_type,
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typename TransformOperator = CGAL::Identity<Image_word_type> >
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void initialize_triangulation_from_labeled_image(C3T3& c3t3,
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const MeshDomain& domain,
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const CGAL::Image_3& image,
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const MeshCriteria& criteria,
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Image_word_type,
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bool protect_features = false
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)
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const MeshDomain& domain,
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const CGAL::Image_3& image,
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const MeshCriteria& criteria,
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Image_word_type,
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bool protect_features = false,
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TransformOperator transform = CGAL::Identity<Image_word_type>())
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{
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typedef typename C3T3::Triangulation Tr;
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typedef typename Tr::Geom_traits Gt;
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@ -111,11 +118,10 @@ void initialize_triangulation_from_labeled_image(C3T3& c3t3,
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Seeds seeds;
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Get_point<Bare_point> get_point(&image);
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std::cout << "Searching for connected components..." << std::endl;
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CGAL::Identity<Image_word_type> no_transformation;
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search_for_connected_components_in_labeled_image(image,
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std::back_inserter(seeds),
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CGAL::Emptyset_iterator(),
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no_transformation,
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transform,
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get_point,
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Image_word_type());
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std::cout << " " << seeds.size() << " components were found." << std::endl;
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