/usr/include/CGAL/Poisson_reconstruction_function.h is in libcgal-dev 4.2-5ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 | // Copyright (c) 2007-09 INRIA (France).
// All rights reserved.
//
// This file is part of CGAL (www.cgal.org).
// You can redistribute it and/or modify it under the terms of the GNU
// General Public License as published by the Free Software Foundation,
// either version 3 of the License, or (at your option) any later version.
//
// Licensees holding a valid commercial license may use this file in
// accordance with the commercial license agreement provided with the software.
//
// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
//
// $URL$
// $Id$
//
// Author(s) : Laurent Saboret, Pierre Alliez
#ifndef CGAL_POISSON_RECONSTRUCTION_FUNCTION_H
#define CGAL_POISSON_RECONSTRUCTION_FUNCTION_H
#ifndef CGAL_DIV_NORMALIZED
# ifndef CGAL_DIV_NON_NORMALIZED
# define CGAL_DIV_NON_NORMALIZED 1
# endif
#endif
#include <vector>
#include <deque>
#include <algorithm>
#include <cmath>
#include <CGAL/trace.h>
#include <CGAL/Reconstruction_triangulation_3.h>
#include <CGAL/spatial_sort.h>
#ifdef CGAL_EIGEN3_ENABLED
#include <CGAL/Eigen_solver_traits.h>
#else
#ifdef CGAL_TAUCS_ENABLED
#include <CGAL/Taucs_solver_traits.h>
#endif
#endif
#include <CGAL/centroid.h>
#include <CGAL/property_map.h>
#include <CGAL/surface_reconstruction_points_assertions.h>
#include <CGAL/poisson_refine_triangulation.h>
#include <CGAL/Robust_circumcenter_filtered_traits_3.h>
#include <CGAL/compute_average_spacing.h>
#include <boost/shared_ptr.hpp>
#include <boost/array.hpp>
#include <boost/type_traits/is_convertible.hpp>
#include <boost/utility/enable_if.hpp>
/*!
\file Poisson_reconstruction_function.h
*/
namespace CGAL {
namespace internal {
template <class RT>
bool
invert(
const RT& a0, const RT& a1, const RT& a2,
const RT& a3, const RT& a4, const RT& a5,
const RT& a6, const RT& a7, const RT& a8,
RT& i0, RT& i1, RT& i2,
RT& i3, RT& i4, RT& i5,
RT& i6, RT& i7, RT& i8)
{
// Compute the adjoint.
i0 = a4*a8 - a5*a7;
i1 = a2*a7 - a1*a8;
i2 = a1*a5 - a2*a4;
i3 = a5*a6 - a3*a8;
i4 = a0*a8 - a2*a6;
i5 = a2*a3 - a0*a5;
i6 = a3*a7 - a4*a6;
i7 = a1*a6 - a0*a7;
i8 = a0*a4 - a1*a3;
RT det = a0*i0 + a1*i3 + a2*i6;
if(det != 0) {
RT idet = (RT(1.0))/det;
i0 *= idet;
i1 *= idet;
i2 *= idet;
i3 *= idet;
i4 *= idet;
i5 *= idet;
i6 *= idet;
i7 *= idet;
i8 *= idet;
return true;
}
return false;
}
}
/// \cond SKIP_IN_MANUAL
struct Poisson_visitor {
void before_insertion() const
{}
};
struct Poisson_skip_vertices {
double ratio;
Random& m_random;
Poisson_skip_vertices(const double ratio, Random& random)
: ratio(ratio), m_random(random) {}
template <typename Iterator>
bool operator()(Iterator) const {
return m_random.get_double() < ratio;
}
};
// Given f1 and f2, two sizing fields, that functor wrapper returns
// max(f1, f2*f2)
// The wrapper stores only pointers to the two functors.
template <typename F1, typename F2>
struct Special_wrapper_of_two_functions_keep_pointers {
F1 *f1;
F2 *f2;
Special_wrapper_of_two_functions_keep_pointers(F1* f1, F2* f2)
: f1(f1), f2(f2) {}
template <typename X>
double operator()(const X& x) const {
return (std::max)((*f1)(x), CGAL::square((*f2)(x)));
}
template <typename X>
double operator()(const X& x) {
return (std::max)((*f1)(x), CGAL::square((*f2)(x)));
}
}; // end struct Special_wrapper_of_two_functions_keep_pointers<F1, F2>
/// \endcond
/*!
\ingroup PkgSurfaceReconstructionFromPointSets
\brief Implementation of the Poisson Surface Reconstruction method.
Given a set of 3D points with oriented normals sampled on the boundary
of a 3D solid, the Poisson Surface Reconstruction method \cite Kazhdan06
solves for an approximate indicator function of the inferred
solid, whose gradient best matches the input normals. The output
scalar function, represented in an adaptive octree, is then
iso-contoured using an adaptive marching cubes.
`Poisson_reconstruction_function` implements a variant of this
algorithm which solves for a piecewise linear function on a 3D
Delaunay triangulation instead of an adaptive octree.
\tparam Gt Geometric traits class.
\cgalModels `ImplicitFunction`
*/
template <class Gt>
class Poisson_reconstruction_function
{
// Public types
public:
/// \name Types
/// @{
typedef Gt Geom_traits; ///< Geometric traits class
/// \cond SKIP_IN_MANUAL
typedef Reconstruction_triangulation_3<Robust_circumcenter_filtered_traits_3<Gt> >
Triangulation;
/// \endcond
typedef typename Triangulation::Cell_handle Cell_handle;
// Geometric types
typedef typename Geom_traits::FT FT; ///< number type.
typedef typename Geom_traits::Point_3 Point; ///< point type.
typedef typename Geom_traits::Vector_3 Vector; ///< vector type.
typedef typename Geom_traits::Sphere_3 Sphere;
/// @}
// Private types
private:
// Internal 3D triangulation, of type Reconstruction_triangulation_3.
// Note: poisson_refine_triangulation() requires a robust circumcenter computation.
// Repeat Triangulation types
typedef typename Triangulation::Triangulation_data_structure Triangulation_data_structure;
typedef typename Geom_traits::Ray_3 Ray;
typedef typename Geom_traits::Plane_3 Plane;
typedef typename Geom_traits::Segment_3 Segment;
typedef typename Geom_traits::Triangle_3 Triangle;
typedef typename Geom_traits::Tetrahedron_3 Tetrahedron;
typedef typename Triangulation::Vertex_handle Vertex_handle;
typedef typename Triangulation::Cell Cell;
typedef typename Triangulation::Vertex Vertex;
typedef typename Triangulation::Facet Facet;
typedef typename Triangulation::Edge Edge;
typedef typename Triangulation::Cell_circulator Cell_circulator;
typedef typename Triangulation::Facet_circulator Facet_circulator;
typedef typename Triangulation::Cell_iterator Cell_iterator;
typedef typename Triangulation::Facet_iterator Facet_iterator;
typedef typename Triangulation::Edge_iterator Edge_iterator;
typedef typename Triangulation::Vertex_iterator Vertex_iterator;
typedef typename Triangulation::Point_iterator Point_iterator;
typedef typename Triangulation::Finite_vertices_iterator Finite_vertices_iterator;
typedef typename Triangulation::Finite_cells_iterator Finite_cells_iterator;
typedef typename Triangulation::Finite_facets_iterator Finite_facets_iterator;
typedef typename Triangulation::Finite_edges_iterator Finite_edges_iterator;
typedef typename Triangulation::All_cells_iterator All_cells_iterator;
typedef typename Triangulation::Locate_type Locate_type;
// Data members.
// Warning: the Surface Mesh Generation package makes copies of implicit functions,
// thus this class must be lightweight and stateless.
private:
// operator() is pre-computed on vertices of *m_tr by solving
// the Poisson equation Laplacian(f) = divergent(normals field).
boost::shared_ptr<Triangulation> m_tr;
mutable boost::shared_ptr<std::vector<boost::array<double,9> > > m_Bary;
mutable std::vector<Point> Dual;
mutable std::vector<Vector> Normal;
// contouring and meshing
Point m_sink; // Point with the minimum value of operator()
mutable Cell_handle m_hint; // last cell found = hint for next search
FT average_spacing;
/// function to be used for the different constructors available that are
/// doing the same thing but with default template parameters
template <typename InputIterator,
typename PointPMap,
typename NormalPMap,
typename Visitor
>
void forward_constructor(
InputIterator first,
InputIterator beyond,
PointPMap point_pmap,
NormalPMap normal_pmap,
Visitor visitor)
{
CGAL::Timer task_timer; task_timer.start();
CGAL_TRACE_STREAM << "Creates Poisson triangulation...\n";
// Inserts points in triangulation
m_tr->insert(
first,beyond,
point_pmap,
normal_pmap,
visitor);
// Prints status
CGAL_TRACE_STREAM << "Creates Poisson triangulation: " << task_timer.time() << " seconds, "
<< std::endl;
}
// Public methods
public:
/// \name Creation
/// @{
/*!
Creates a Poisson implicit function from the range of points `[first, beyond)`.
\tparam InputIterator iterator over input points.
\tparam PointPMap is a model of `ReadablePropertyMap` with
a `value_type = Point`. It can be omitted if `InputIterator`
`value_type` is convertible to `Point`.
\tparam NormalPMap is a model of `ReadablePropertyMap`
with a `value_type = Vector`.
*/
template <typename InputIterator,
typename PointPMap,
typename NormalPMap
>
Poisson_reconstruction_function(
InputIterator first, ///< iterator over the first input point.
InputIterator beyond, ///< past-the-end iterator over the input points.
PointPMap point_pmap, ///< property map to access the position of an input point.
NormalPMap normal_pmap ///< property map to access the *oriented* normal of an input point.
)
: m_tr(new Triangulation), m_Bary(new std::vector<boost::array<double,9> > )
, average_spacing(CGAL::compute_average_spacing(first, beyond, 6))
{
forward_constructor(first, beyond, point_pmap, normal_pmap, Poisson_visitor());
}
/// \cond SKIP_IN_MANUAL
template <typename InputIterator,
typename PointPMap,
typename NormalPMap,
typename Visitor
>
Poisson_reconstruction_function(
InputIterator first, ///< iterator over the first input point.
InputIterator beyond, ///< past-the-end iterator over the input points.
PointPMap point_pmap, ///< property map to access the position of an input point.
NormalPMap normal_pmap, ///< property map to access the *oriented* normal of an input point.
Visitor visitor)
: m_tr(new Triangulation), m_Bary(new std::vector<boost::array<double,9> > )
, average_spacing(CGAL::compute_average_spacing(first, beyond, 6))
{
forward_constructor(first, beyond, point_pmap, normal_pmap, visitor);
}
// This variant creates a default point property map = Dereference_property_map and Visitor=Poisson_visitor
template <typename InputIterator,
typename NormalPMap
>
Poisson_reconstruction_function(
InputIterator first, ///< iterator over the first input point.
InputIterator beyond, ///< past-the-end iterator over the input points.
NormalPMap normal_pmap, ///< property map to access the *oriented* normal of an input point.
typename boost::enable_if<
boost::is_convertible<typename InputIterator::value_type, Point>
>::type* = 0
)
: m_tr(new Triangulation), m_Bary(new std::vector<boost::array<double,9> > )
, average_spacing(CGAL::compute_average_spacing(first, beyond, 6))
{
forward_constructor(first, beyond, make_dereference_property_map(first), normal_pmap, Poisson_visitor());
CGAL::Timer task_timer; task_timer.start();
}
/// \endcond
/// @}
/// \name Operations
/// @{
/// Returns a sphere bounding the inferred surface.
Sphere bounding_sphere() const
{
return m_tr->bounding_sphere();
}
/// \cond SKIP_IN_MANUAL
const Triangulation& tr() const {
return *m_tr;
}
// This variant requires all parameters.
template <class SparseLinearAlgebraTraits_d,
class Visitor>
bool compute_implicit_function(
SparseLinearAlgebraTraits_d solver,// = SparseLinearAlgebraTraits_d(),
Visitor visitor,
double approximation_ratio = 0,
double average_spacing_ratio = 5)
{
CGAL::Timer task_timer; task_timer.start();
CGAL_TRACE_STREAM << "Delaunay refinement...\n";
// Delaunay refinement
const FT radius_edge_ratio_bound = 2.5;
const unsigned int max_vertices = (unsigned int)1e7; // max 10M vertices
const FT enlarge_ratio = 1.5;
const FT radius = sqrt(bounding_sphere().squared_radius()); // get triangulation's radius
const FT cell_radius_bound = radius/5.; // large
internal::Poisson::Constant_sizing_field<Triangulation> sizing_field(CGAL::square(cell_radius_bound));
std::vector<int> NB;
NB.push_back( delaunay_refinement(radius_edge_ratio_bound,sizing_field,max_vertices,enlarge_ratio));
while(m_tr->insert_fraction(visitor)){
NB.push_back( delaunay_refinement(radius_edge_ratio_bound,sizing_field,max_vertices,enlarge_ratio));
}
if(approximation_ratio > 0. &&
approximation_ratio * std::distance(m_tr->input_points_begin(),
m_tr->input_points_end()) > 20) {
// Add a pass of Delaunay refinement.
//
// In that pass, the sizing field, of the refinement process of the
// triangulation, is based on the result of a poisson function with a
// sample of the input points. The ratio is 'approximation_ratio'.
//
// For optimization reasons, the cell criteria of the refinement
// process uses two sizing fields:
//
// - the minimum of the square of 'coarse_poisson_function' and the
// square of the constant field equal to 'average_spacing',
//
// - a second sizing field that is constant, and equal to:
//
// average_spacing*average_spacing_ratio
//
// If a given cell is smaller than the constant second sizing field,
// then the cell is considered as small enough, and the first sizing
// field, more costly, is not evaluated.
typedef Filter_iterator<typename Triangulation::Input_point_iterator,
Poisson_skip_vertices> Some_points_iterator;
//make it deterministic
Random random(0);
Poisson_skip_vertices skip(1.-approximation_ratio,random);
CGAL_TRACE_STREAM << "SPECIAL PASS that uses an approximation of the result (approximation ratio: "
<< approximation_ratio << ")" << std::endl;
CGAL::Timer approximation_timer; approximation_timer.start();
CGAL::Timer sizing_field_timer; sizing_field_timer.start();
Poisson_reconstruction_function<Geom_traits>
coarse_poisson_function(Some_points_iterator(m_tr->input_points_end(),
skip,
m_tr->input_points_begin()),
Some_points_iterator(m_tr->input_points_end(),
skip),
Normal_of_point_with_normal_pmap<Geom_traits>() );
coarse_poisson_function.compute_implicit_function(solver, Poisson_visitor(),
0.);
internal::Poisson::Constant_sizing_field<Triangulation>
min_sizing_field(CGAL::square(average_spacing));
internal::Poisson::Constant_sizing_field<Triangulation>
sizing_field_ok(CGAL::square(average_spacing*average_spacing_ratio));
Special_wrapper_of_two_functions_keep_pointers<
internal::Poisson::Constant_sizing_field<Triangulation>,
Poisson_reconstruction_function<Geom_traits> > sizing_field2(&min_sizing_field,
&coarse_poisson_function);
sizing_field_timer.stop();
std::cerr << "Construction time of the sizing field: " << sizing_field_timer.time()
<< " seconds" << std::endl;
NB.push_back( delaunay_refinement(radius_edge_ratio_bound,
sizing_field2,
max_vertices,
enlarge_ratio,
sizing_field_ok) );
approximation_timer.stop();
CGAL_TRACE_STREAM << "SPECIAL PASS END (" << approximation_timer.time() << " seconds)" << std::endl;
}
// Prints status
CGAL_TRACE_STREAM << "Delaunay refinement: " << "added ";
for(std::size_t i = 0; i < NB.size()-1; i++){
CGAL_TRACE_STREAM << NB[i] << " + ";
}
CGAL_TRACE_STREAM << NB.back() << " Steiner points, "
<< task_timer.time() << " seconds, "
<< std::endl;
task_timer.reset();
#ifdef CGAL_DIV_NON_NORMALIZED
CGAL_TRACE_STREAM << "Solve Poisson equation with non-normalized divergence...\n";
#else
CGAL_TRACE_STREAM << "Solve Poisson equation with normalized divergence...\n";
#endif
// Computes the Poisson indicator function operator()
// at each vertex of the triangulation.
double lambda = 0.1;
if ( ! solve_poisson(solver, lambda) )
{
std::cerr << "Error: cannot solve Poisson equation" << std::endl;
return false;
}
// Shift and orient operator() such that:
// - operator() = 0 on the input points,
// - operator() < 0 inside the surface.
set_contouring_value(median_value_at_input_vertices());
// Prints status
CGAL_TRACE_STREAM << "Solve Poisson equation: " << task_timer.time() << " seconds, "
<< std::endl;
task_timer.reset();
return true;
}
/// \endcond
/*!
This function must be called after the
insertion of oriented points. It computes the piecewise linear scalar
function operator() by: applying Delaunay refinement, solving for
operator() at each vertex of the triangulation with a sparse linear
solver, and shifting and orienting operator() such that it is 0 at all
input points and negative inside the inferred surface.
\tparam SparseLinearAlgebraTraits_d Symmetric definite positive sparse linear solver.
If \ref thirdpartyEigen "Eigen" 3.1 (or greater) is available and `CGAL_EIGEN3_ENABLED`
is defined, an overload with \link Eigen_solver_traits <tt>Eigen_solver_traits<Eigen::ConjugateGradient<Eigen_sparse_symmetric_matrix<double>::EigenType> ></tt> \endlink
as default solver is provided.
\param solver sparse linear solver.
\param smoother_hole_filling controls if the Delaunay refinement is done for the input points, or for an approximation of the surface obtained from a first pass of the algorithm on a sample of the points.
\return `false` if the linear solver fails.
*/
template <class SparseLinearAlgebraTraits_d>
bool compute_implicit_function(SparseLinearAlgebraTraits_d solver, bool smoother_hole_filling = false)
{
if (smoother_hole_filling)
return compute_implicit_function<SparseLinearAlgebraTraits_d,Poisson_visitor>(solver,Poisson_visitor(),0.02,5);
else
return compute_implicit_function<SparseLinearAlgebraTraits_d,Poisson_visitor>(solver,Poisson_visitor());
}
/// \cond SKIP_IN_MANUAL
#ifdef CGAL_EIGEN3_ENABLED
// This variant provides the default sparse linear traits class = Eigen_solver_traits.
bool compute_implicit_function(bool smoother_hole_filling = false)
{
typedef Eigen_solver_traits<Eigen::ConjugateGradient<Eigen_sparse_symmetric_matrix<double>::EigenType> > Solver;
return compute_implicit_function<Solver>(Solver(), smoother_hole_filling);
}
#else
#ifdef CGAL_TAUCS_ENABLED
// This variant provides the default sparse linear traits class = Taucs_symmetric_solver_traits.
bool compute_implicit_function(bool smoother_hole_filling = false)
{
typedef Taucs_symmetric_solver_traits<double> Solver;
return compute_implicit_function<Solver>(Solver(), smoother_hole_filling);
}
#endif
#endif
boost::tuple<FT, Cell_handle, bool> special_func(const Point& p) const
{
m_hint = m_tr->locate(p ,m_hint ); // no hint when we use hierarchy
if(m_tr->is_infinite(m_hint)) {
int i = m_hint->index(m_tr->infinite_vertex());
return boost::make_tuple(m_hint->vertex((i+1)&3)->f(),
m_hint, true);
}
FT a,b,c,d;
barycentric_coordinates(p,m_hint,a,b,c,d);
return boost::make_tuple(a * m_hint->vertex(0)->f() +
b * m_hint->vertex(1)->f() +
c * m_hint->vertex(2)->f() +
d * m_hint->vertex(3)->f(),
m_hint, false);
}
/// \endcond
/*!
`ImplicitFunction` interface: evaluates the implicit function at a
given 3D query point. The function `compute_implicit_function` must be
called before the first call to `operator()`.
*/
FT operator()(const Point& p) const
{
m_hint = m_tr->locate(p ,m_hint);
if(m_tr->is_infinite(m_hint)) {
int i = m_hint->index(m_tr->infinite_vertex());
return m_hint->vertex((i+1)&3)->f();
}
FT a,b,c,d;
barycentric_coordinates(p,m_hint,a,b,c,d);
return a * m_hint->vertex(0)->f() +
b * m_hint->vertex(1)->f() +
c * m_hint->vertex(2)->f() +
d * m_hint->vertex(3)->f();
}
/// \cond SKIP_IN_MANUAL
void initialize_cell_indices()
{
int i=0;
for(Finite_cells_iterator fcit = m_tr->finite_cells_begin();
fcit != m_tr->finite_cells_end();
++fcit){
fcit->info()= i++;
}
}
void initialize_barycenters() const
{
m_Bary->resize(m_tr->number_of_cells());
for(std::size_t i=0; i< m_Bary->size();i++){
(*m_Bary)[i][0]=-1;
}
}
void initialize_cell_normals() const
{
Normal.resize(m_tr->number_of_cells());
int i = 0;
int N = 0;
for(Finite_cells_iterator fcit = m_tr->finite_cells_begin();
fcit != m_tr->finite_cells_end();
++fcit){
Normal[i] = cell_normal(fcit);
if(Normal[i] == NULL_VECTOR){
N++;
}
++i;
}
std::cerr << N << " out of " << i << " cells have NULL_VECTOR as normal" << std::endl;
}
void initialize_duals() const
{
Dual.resize(m_tr->number_of_cells());
int i = 0;
for(Finite_cells_iterator fcit = m_tr->finite_cells_begin();
fcit != m_tr->finite_cells_end();
++fcit){
Dual[i++] = m_tr->dual(fcit);
}
}
void clear_duals() const
{
Dual.clear();
}
void clear_normals() const
{
Normal.clear();
}
void initialize_matrix_entry(Cell_handle ch) const
{
boost::array<double,9> & entry = (*m_Bary)[ch->info()];
const Point& pa = ch->vertex(0)->point();
const Point& pb = ch->vertex(1)->point();
const Point& pc = ch->vertex(2)->point();
const Point& pd = ch->vertex(3)->point();
Vector va = pa - pd;
Vector vb = pb - pd;
Vector vc = pc - pd;
internal::invert(va.x(), va.y(), va.z(),
vb.x(), vb.y(), vb.z(),
vc.x(), vc.y(), vc.z(),
entry[0],entry[1],entry[2],entry[3],entry[4],entry[5],entry[6],entry[7],entry[8]);
}
/// \endcond
/// Returns a point located inside the inferred surface.
Point get_inner_point() const
{
// Gets point / the implicit function is minimum
return m_sink;
}
/// @}
// Private methods:
private:
/// Delaunay refinement (break bad tetrahedra, where
/// bad means badly shaped or too big). The normal of
/// Steiner points is set to zero.
/// Returns the number of vertices inserted.
template <typename Sizing_field>
unsigned int delaunay_refinement(FT radius_edge_ratio_bound, ///< radius edge ratio bound (ignored if zero)
Sizing_field sizing_field, ///< cell radius bound (ignored if zero)
unsigned int max_vertices, ///< number of vertices bound
FT enlarge_ratio) ///< bounding box enlarge ratio
{
return delaunay_refinement(radius_edge_ratio_bound,
sizing_field,
max_vertices,
enlarge_ratio,
internal::Poisson::Constant_sizing_field<Triangulation>());
}
template <typename Sizing_field,
typename Second_sizing_field>
unsigned int delaunay_refinement(FT radius_edge_ratio_bound, ///< radius edge ratio bound (ignored if zero)
Sizing_field sizing_field, ///< cell radius bound (ignored if zero)
unsigned int max_vertices, ///< number of vertices bound
FT enlarge_ratio, ///< bounding box enlarge ratio
Second_sizing_field second_sizing_field)
{
Sphere elarged_bsphere = enlarged_bounding_sphere(enlarge_ratio);
unsigned int nb_vertices_added = poisson_refine_triangulation(*m_tr,radius_edge_ratio_bound,sizing_field,second_sizing_field,max_vertices,elarged_bsphere);
return nb_vertices_added;
}
/// Poisson reconstruction.
/// Returns false on error.
///
/// @commentheading Template parameters:
/// @param SparseLinearAlgebraTraits_d Symmetric definite positive sparse linear solver.
template <class SparseLinearAlgebraTraits_d>
bool solve_poisson(
SparseLinearAlgebraTraits_d solver, ///< sparse linear solver
double lambda)
{
CGAL_TRACE("Calls solve_poisson()\n");
double time_init = clock();
double duration_assembly = 0.0;
double duration_solve = 0.0;
initialize_cell_indices();
initialize_barycenters();
// get #variables
constrain_one_vertex_on_convex_hull();
m_tr->index_unconstrained_vertices();
unsigned int nb_variables = static_cast<unsigned int>(m_tr->number_of_vertices()-1);
CGAL_TRACE(" Number of variables: %ld\n", (long)(nb_variables));
// Assemble linear system A*X=B
typename SparseLinearAlgebraTraits_d::Matrix A(nb_variables); // matrix is symmetric definite positive
typename SparseLinearAlgebraTraits_d::Vector X(nb_variables), B(nb_variables);
initialize_duals();
#ifndef CGAL_DIV_NON_NORMALIZED
initialize_cell_normals();
#endif
Finite_vertices_iterator v, e;
for(v = m_tr->finite_vertices_begin(),
e = m_tr->finite_vertices_end();
v != e;
++v)
{
if(!m_tr->is_constrained(v)) {
#ifdef CGAL_DIV_NON_NORMALIZED
B[v->index()] = div(v); // rhs -> divergent
#else // not defined(CGAL_DIV_NORMALIZED)
B[v->index()] = div_normalized(v); // rhs -> divergent
#endif // not defined(CGAL_DIV_NORMALIZED)
assemble_poisson_row<SparseLinearAlgebraTraits_d>(A,v,B,lambda);
}
}
clear_duals();
clear_normals();
duration_assembly = (clock() - time_init)/CLOCKS_PER_SEC;
CGAL_TRACE(" Creates matrix: done (%.2lf s)\n", duration_assembly);
CGAL_TRACE(" Solve sparse linear system...\n");
// Solve "A*X = B". On success, solution is (1/D) * X.
time_init = clock();
double D;
if(!solver.linear_solver(A, B, X, D))
return false;
CGAL_surface_reconstruction_points_assertion(D == 1.0);
duration_solve = (clock() - time_init)/CLOCKS_PER_SEC;
CGAL_TRACE(" Solve sparse linear system: done (%.2lf s)\n", duration_solve);
// copy function's values to vertices
unsigned int index = 0;
for (v = m_tr->finite_vertices_begin(), e = m_tr->finite_vertices_end(); v!= e; ++v)
if(!m_tr->is_constrained(v))
v->f() = X[index++];
CGAL_TRACE("End of solve_poisson()\n");
return true;
}
/// Shift and orient the implicit function such that:
/// - the implicit function = 0 for points / f() = contouring_value,
/// - the implicit function < 0 inside the surface.
///
/// Returns the minimum value of the implicit function.
FT set_contouring_value(FT contouring_value)
{
// median value set to 0.0
shift_f(-contouring_value);
// check value on convex hull (should be positive)
Vertex_handle v = any_vertex_on_convex_hull();
if(v->f() < 0.0)
flip_f();
// Update m_sink
FT sink_value = find_sink();
return sink_value;
}
/// Gets median value of the implicit function over input vertices.
FT median_value_at_input_vertices() const
{
std::deque<FT> values;
Finite_vertices_iterator v, e;
for(v = m_tr->finite_vertices_begin(),
e= m_tr->finite_vertices_end();
v != e;
v++)
if(v->type() == Triangulation::INPUT)
values.push_back(v->f());
std::size_t size = values.size();
if(size == 0)
{
std::cerr << "Contouring: no input points\n";
return 0.0;
}
std::sort(values.begin(),values.end());
std::size_t index = size/2;
// return values[size/2];
return 0.5 * (values[index] + values[index+1]); // avoids singular cases
}
void barycentric_coordinates(const Point& p,
Cell_handle cell,
FT& a,
FT& b,
FT& c,
FT& d) const
{
// const Point& pa = cell->vertex(0)->point();
// const Point& pb = cell->vertex(1)->point();
// const Point& pc = cell->vertex(2)->point();
const Point& pd = cell->vertex(3)->point();
#if 1
//Vector va = pa - pd;
//Vector vb = pb - pd;
//Vector vc = pc - pd;
Vector vp = p - pd;
//FT i00, i01, i02, i10, i11, i12, i20, i21, i22;
//internal::invert(va.x(), va.y(), va.z(),
// vb.x(), vb.y(), vb.z(),
// vc.x(), vc.y(), vc.z(),
// i00, i01, i02, i10, i11, i12, i20, i21, i22);
const boost::array<double,9> & i = (*m_Bary)[cell->info()];
if(i[0]==-1){
initialize_matrix_entry(cell);
}
// UsedBary[cell->info()] = true;
a = i[0] * vp.x() + i[3] * vp.y() + i[6] * vp.z();
b = i[1] * vp.x() + i[4] * vp.y() + i[7] * vp.z();
c = i[2] * vp.x() + i[5] * vp.y() + i[8] * vp.z();
d = 1 - ( a + b + c);
#else
FT v = volume(pa,pb,pc,pd);
a = std::fabs(volume(pb,pc,pd,p) / v);
b = std::fabs(volume(pa,pc,pd,p) / v);
c = std::fabs(volume(pb,pa,pd,p) / v);
d = std::fabs(volume(pb,pc,pa,p) / v);
std::cerr << "_________________________________\n";
std::cerr << aa << " " << bb << " " << cc << " " << dd << std::endl;
std::cerr << a << " " << b << " " << c << " " << d << std::endl;
#endif
}
FT find_sink()
{
m_sink = CGAL::ORIGIN;
FT min_f = 1e38;
Finite_vertices_iterator v, e;
for(v = m_tr->finite_vertices_begin(),
e= m_tr->finite_vertices_end();
v != e;
v++)
{
if(v->f() < min_f)
{
m_sink = v->point();
min_f = v->f();
}
}
return min_f;
}
void shift_f(const FT shift)
{
Finite_vertices_iterator v, e;
for(v = m_tr->finite_vertices_begin(),
e = m_tr->finite_vertices_end();
v!= e;
v++)
v->f() += shift;
}
void flip_f()
{
Finite_vertices_iterator v, e;
for(v = m_tr->finite_vertices_begin(),
e = m_tr->finite_vertices_end();
v != e;
v++)
v->f() = -v->f();
}
Vertex_handle any_vertex_on_convex_hull()
{
Cell_handle ch = m_tr->infinite_vertex()->cell();
return ch->vertex( (ch->index( m_tr->infinite_vertex())+1)%4);
}
void constrain_one_vertex_on_convex_hull(const FT value = 0.0)
{
Vertex_handle v = any_vertex_on_convex_hull();
m_tr->constrain(v);
v->f() = value;
}
// TODO: Some entities are computed too often
// - nn and area should not be computed for the face and its opposite face
//
// divergent
FT div_normalized(Vertex_handle v)
{
std::vector<Cell_handle> cells;
cells.reserve(32);
m_tr->incident_cells(v,std::back_inserter(cells));
FT div = 0;
typename std::vector<Cell_handle>::iterator it;
for(it = cells.begin(); it != cells.end(); it++)
{
Cell_handle cell = *it;
if(m_tr->is_infinite(cell))
continue;
// compute average normal per cell
Vector n = get_cell_normal(cell);
// zero normal - no need to compute anything else
if(n == CGAL::NULL_VECTOR)
continue;
// compute n'
int index = cell->index(v);
const Point& x = cell->vertex(index)->point();
const Point& a = cell->vertex((index+1)%4)->point();
const Point& b = cell->vertex((index+2)%4)->point();
const Point& c = cell->vertex((index+3)%4)->point();
Vector nn = (index%2==0) ? CGAL::cross_product(b-a,c-a) : CGAL::cross_product(c-a,b-a);
nn = nn / std::sqrt(nn*nn); // normalize
Vector p = a - x;
Vector q = b - x;
Vector r = c - x;
FT p_n = std::sqrt(p*p);
FT q_n = std::sqrt(q*q);
FT r_n = std::sqrt(r*r);
FT solid_angle = p*(CGAL::cross_product(q,r));
solid_angle = std::abs(solid_angle / (p_n*q_n*r_n + (p*q)*r_n + (q*r)*p_n + (r*p)*q_n));
FT area = std::sqrt(squared_area(a,b,c));
FT length = p_n + q_n + r_n;
div += n * nn * area / length ;
}
return div * FT(3.0);
}
FT div(Vertex_handle v)
{
std::vector<Cell_handle> cells;
cells.reserve(32);
m_tr->incident_cells(v,std::back_inserter(cells));
FT div = 0.0;
typename std::vector<Cell_handle>::iterator it;
for(it = cells.begin(); it != cells.end(); it++)
{
Cell_handle cell = *it;
if(m_tr->is_infinite(cell))
continue;
const int index = cell->index(v);
const Point& a = cell->vertex(m_tr->vertex_triple_index(index, 0))->point();
const Point& b = cell->vertex(m_tr->vertex_triple_index(index, 1))->point();
const Point& c = cell->vertex(m_tr->vertex_triple_index(index, 2))->point();
const Vector nn = CGAL::cross_product(b-a,c-a);
div+= nn * (//v->normal() +
cell->vertex((index+1)%4)->normal() +
cell->vertex((index+2)%4)->normal() +
cell->vertex((index+3)%4)->normal());
}
return div;
}
Vector get_cell_normal(Cell_handle cell)
{
return Normal[cell->info()];
}
Vector cell_normal(Cell_handle cell) const
{
const Vector& n0 = cell->vertex(0)->normal();
const Vector& n1 = cell->vertex(1)->normal();
const Vector& n2 = cell->vertex(2)->normal();
const Vector& n3 = cell->vertex(3)->normal();
Vector n = n0 + n1 + n2 + n3;
if(n != NULL_VECTOR){
FT sq_norm = n*n;
if(sq_norm != 0.0){
return n / std::sqrt(sq_norm); // normalize
}
}
return NULL_VECTOR;
}
// cotan formula as area(voronoi face) / len(primal edge)
FT cotan_geometric(Edge& edge)
{
Cell_handle cell = edge.first;
Vertex_handle vi = cell->vertex(edge.second);
Vertex_handle vj = cell->vertex(edge.third);
// primal edge
const Point& pi = vi->point();
const Point& pj = vj->point();
Vector primal = pj - pi;
FT len_primal = std::sqrt(primal * primal);
return area_voronoi_face(edge) / len_primal;
}
// spin around edge
// return area(voronoi face)
FT area_voronoi_face(Edge& edge)
{
// circulate around edge
Cell_circulator circ = m_tr->incident_cells(edge);
Cell_circulator done = circ;
std::vector<Point> voronoi_points;
voronoi_points.reserve(9);
do
{
Cell_handle cell = circ;
if(!m_tr->is_infinite(cell))
voronoi_points.push_back(Dual[cell->info()]);
else // one infinite tet, switch to another calculation
return area_voronoi_face_boundary(edge);
circ++;
}
while(circ != done);
if(voronoi_points.size() < 3)
{
CGAL_surface_reconstruction_points_assertion(false);
return 0.0;
}
// sum up areas
FT area = 0.0;
const Point& a = voronoi_points[0];
std::size_t nb_triangles = voronoi_points.size() - 1;
for(std::size_t i=1;i<nb_triangles;i++)
{
const Point& b = voronoi_points[i];
const Point& c = voronoi_points[i+1];
area += std::sqrt(squared_area(a,b,c));
}
return area;
}
// approximate area when a cell is infinite
FT area_voronoi_face_boundary(Edge& edge)
{
FT area = 0.0;
Vertex_handle vi = edge.first->vertex(edge.second);
Vertex_handle vj = edge.first->vertex(edge.third);
const Point& pi = vi->point();
const Point& pj = vj->point();
Point m = CGAL::midpoint(pi,pj);
// circulate around each incident cell
Cell_circulator circ = m_tr->incident_cells(edge);
Cell_circulator done = circ;
do
{
Cell_handle cell = circ;
if(!m_tr->is_infinite(cell))
{
// circumcenter of cell
Point c = Dual[cell->info()];
Tetrahedron tet = m_tr->tetrahedron(cell);
int i = cell->index(vi);
int j = cell->index(vj);
int k = Triangulation_utils_3::next_around_edge(i,j);
int l = Triangulation_utils_3::next_around_edge(j,i);
Vertex_handle vk = cell->vertex(k);
Vertex_handle vl = cell->vertex(l);
const Point& pk = vk->point();
const Point& pl = vl->point();
// if circumcenter is outside tet
// pick barycenter instead
if(tet.has_on_unbounded_side(c))
{
Point cell_points[4] = {pi,pj,pk,pl};
c = CGAL::centroid(cell_points, cell_points+4);
}
Point ck = CGAL::circumcenter(pi,pj,pk);
Point cl = CGAL::circumcenter(pi,pj,pl);
area += std::sqrt(squared_area(m,c,ck));
area += std::sqrt(squared_area(m,c,cl));
}
circ++;
}
while(circ != done);
return area;
}
/// Assemble vi's row of the linear system A*X=B
///
/// @commentheading Template parameters:
/// @param SparseLinearAlgebraTraits_d Symmetric definite positive sparse linear solver.
template <class SparseLinearAlgebraTraits_d>
void assemble_poisson_row(typename SparseLinearAlgebraTraits_d::Matrix& A,
Vertex_handle vi,
typename SparseLinearAlgebraTraits_d::Vector& B,
double lambda)
{
// for each vertex vj neighbor of vi
std::vector<Edge> edges;
m_tr->incident_edges(vi,std::back_inserter(edges));
double diagonal = 0.0;
for(typename std::vector<Edge>::iterator it = edges.begin();
it != edges.end();
it++)
{
Vertex_handle vj = it->first->vertex(it->third);
if(vj == vi){
vj = it->first->vertex(it->second);
}
if(m_tr->is_infinite(vj))
continue;
// get corresponding edge
Edge edge( it->first, it->first->index(vi), it->first->index(vj));
if(vi->index() < vj->index()){
std::swap(edge.second, edge.third);
}
double cij = cotan_geometric(edge);
if(m_tr->is_constrained(vj)){
if(! is_valid(vj->f())){
std::cerr << "vj->f() = " << vj->f() << " is not valid" << std::endl;
}
B[vi->index()] -= cij * vj->f(); // change rhs
if(! is_valid( B[vi->index()])){
std::cerr << " B[vi->index()] = " << B[vi->index()] << " is not valid" << std::endl;
}
} else {
if(! is_valid(cij)){
std::cerr << "cij = " << cij << " is not valid" << std::endl;
}
A.set_coef(vi->index(),vj->index(), -cij, true /*new*/); // off-diagonal coefficient
}
diagonal += cij;
}
// diagonal coefficient
if (vi->type() == Triangulation::INPUT){
A.set_coef(vi->index(),vi->index(), diagonal + lambda, true /*new*/) ;
} else{
A.set_coef(vi->index(),vi->index(), diagonal, true /*new*/);
}
}
/// Computes enlarged geometric bounding sphere of the embedded triangulation.
Sphere enlarged_bounding_sphere(FT ratio) const
{
Sphere bsphere = bounding_sphere(); // triangulation's bounding sphere
return Sphere(bsphere.center(), bsphere.squared_radius() * ratio*ratio);
}
}; // end of Poisson_reconstruction_function
} //namespace CGAL
#endif // CGAL_POISSON_RECONSTRUCTION_FUNCTION_H
|