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-rw-r--r--src/Alpha_complex/include/gudhi/Alpha_complex_3d.h75
1 files changed, 34 insertions, 41 deletions
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
index c19ebb79..562ef139 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
@@ -12,8 +12,10 @@
#ifndef ALPHA_COMPLEX_3D_H_
#define ALPHA_COMPLEX_3D_H_
-#include <boost/version.hpp>
#include <boost/variant.hpp>
+#include <boost/range/size.hpp>
+#include <boost/range/combine.hpp>
+#include <boost/range/adaptor/transformed.hpp>
#include <gudhi/Debug_utils.h>
#include <gudhi/Alpha_complex_options.h>
@@ -35,8 +37,6 @@
#include <CGAL/iterator.h>
#include <CGAL/version.h> // for CGAL_VERSION_NR
-#include <Eigen/src/Core/util/Macros.h> // for EIGEN_VERSION_AT_LEAST
-
#include <boost/container/static_vector.hpp>
#include <iostream>
@@ -53,16 +53,10 @@
# error Alpha_complex_3d is only available for CGAL >= 4.11
#endif
-#if !EIGEN_VERSION_AT_LEAST(3,1,0)
-# error Alpha_complex_3d is only available for Eigen3 >= 3.1.0 installed with CGAL
-#endif
-
namespace Gudhi {
namespace alpha_complex {
-thread_local double RELATIVE_PRECISION_OF_TO_DOUBLE = 0.00001;
-
// Value_from_iterator returns the filtration value from an iterator on alpha shapes values
//
// FAST SAFE EXACT
@@ -104,7 +98,7 @@ struct Value_from_iterator<complexity::EXACT> {
* \tparam Periodic Boolean used to set/unset the periodic version of Alpha_complex_3d. Default value is false.
*
* For the weighted version, weights values are explained on CGAL
- * <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0">Alpha shapes 3d</a> and
+ * <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#Alpha_shapes_3Definitions">Alpha shapes 3d</a> and
* <a href="https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation">Regular
* triangulation</a> documentation.
*
@@ -157,8 +151,10 @@ class Alpha_complex_3d {
using Kernel = CGAL::Periodic_3_regular_triangulation_traits_3<Predicates>;
};
+ public:
using Kernel = typename Kernel_3<Predicates, Weighted, Periodic>::Kernel;
+ private:
using TdsVb = typename std::conditional<Periodic, CGAL::Periodic_3_triangulation_ds_vertex_base_3<>,
CGAL::Triangulation_ds_vertex_base_3<>>::type;
@@ -277,8 +273,8 @@ Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Bare_
Alpha_complex_3d(const InputPointRange& points) {
static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d");
- alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(
- new Alpha_shape_3(std::begin(points), std::end(points), 0, Alpha_shape_3::GENERAL));
+ alpha_shape_3_ptr_ = std::make_unique<Alpha_shape_3>(
+ std::begin(points), std::end(points), 0, Alpha_shape_3::GENERAL);
}
/** \brief Alpha_complex constructor from a list of points and associated weights.
@@ -299,20 +295,15 @@ Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Bare_
Alpha_complex_3d(const InputPointRange& points, WeightRange weights) {
static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d");
static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d");
- GUDHI_CHECK((weights.size() == points.size()),
+ // FIXME: this test is only valid if we have a forward range
+ GUDHI_CHECK(boost::size(weights) == boost::size(points),
std::invalid_argument("Points number in range different from weights range number"));
- std::vector<Weighted_point_3> weighted_points_3;
+ auto weighted_points_3 = boost::range::combine(points, weights)
+ | boost::adaptors::transformed([](auto const&t){return Weighted_point_3(boost::get<0>(t), boost::get<1>(t));});
- std::size_t index = 0;
- weighted_points_3.reserve(points.size());
- while ((index < weights.size()) && (index < points.size())) {
- weighted_points_3.push_back(Weighted_point_3(points[index], weights[index]));
- index++;
- }
-
- alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(
- new Alpha_shape_3(std::begin(weighted_points_3), std::end(weighted_points_3), 0, Alpha_shape_3::GENERAL));
+ alpha_shape_3_ptr_ = std::make_unique<Alpha_shape_3>(
+ std::begin(weighted_points_3), std::end(weighted_points_3), 0, Alpha_shape_3::GENERAL);
}
/** \brief Alpha_complex constructor from a list of points and an iso-cuboid coordinates.
@@ -356,7 +347,7 @@ Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Bare_
// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
// Maybe need to set it to GENERAL mode
- alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(new Alpha_shape_3(pdt, 0, Alpha_shape_3::GENERAL));
+ alpha_shape_3_ptr_ = std::make_unique<Alpha_shape_3>(pdt, 0, Alpha_shape_3::GENERAL);
}
/** \brief Alpha_complex constructor from a list of points, associated weights and an iso-cuboid coordinates.
@@ -388,31 +379,27 @@ Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Bare_
FT z_min, FT x_max, FT y_max, FT z_max) {
static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d");
static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d");
- GUDHI_CHECK((weights.size() == points.size()),
+ // FIXME: this test is only valid if we have a forward range
+ GUDHI_CHECK(boost::size(weights) == boost::size(points),
std::invalid_argument("Points number in range different from weights range number"));
// Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
GUDHI_CHECK(
(x_max - x_min == y_max - y_min) && (x_max - x_min == z_max - z_min) && (z_max - z_min == y_max - y_min),
std::invalid_argument("The size of the cuboid in every directions is not the same."));
- std::vector<Weighted_point_3> weighted_points_3;
-
- std::size_t index = 0;
- weighted_points_3.reserve(points.size());
-
#ifdef GUDHI_DEBUG
// Defined in GUDHI_DEBUG to avoid unused variable warning for GUDHI_CHECK
FT maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);
#endif
- while ((index < weights.size()) && (index < points.size())) {
- GUDHI_CHECK((weights[index] < maximal_possible_weight) && (weights[index] >= 0),
- std::invalid_argument("Invalid weight at index " + std::to_string(index + 1) +
- ". Must be positive and less than maximal possible weight = 1/64*cuboid length "
- "squared, which is not an acceptable input."));
- weighted_points_3.push_back(Weighted_point_3(points[index], weights[index]));
- index++;
- }
+ auto weighted_points_3 = boost::range::combine(points, weights)
+ | boost::adaptors::transformed([=](auto const&t){
+ auto w = boost::get<1>(t);
+ GUDHI_CHECK((w < maximal_possible_weight) && (w >= 0),
+ std::invalid_argument("Invalid weight " + std::to_string(w) +
+ ". Must be non-negative and less than maximal possible weight = 1/64*cuboid length squared."));
+ return Weighted_point_3(boost::get<0>(t), w);
+ });
// Define the periodic cube
Dt pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
@@ -426,7 +413,7 @@ Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Bare_
// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
// Maybe need to set it to GENERAL mode
- alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(new Alpha_shape_3(pdt, 0, Alpha_shape_3::GENERAL));
+ alpha_shape_3_ptr_ = std::make_unique<Alpha_shape_3>(pdt, 0, Alpha_shape_3::GENERAL);
}
/** \brief Inserts all Delaunay triangulation into the simplicial complex.
@@ -471,6 +458,10 @@ Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Bare_
#ifdef DEBUG_TRACES
std::clog << "filtration_with_alpha_values returns : " << objects.size() << " objects" << std::endl;
#endif // DEBUG_TRACES
+ if (objects.size() == 0) {
+ std::cerr << "Alpha_complex_3d create_complex - no triangulation as points are on a 2d plane\n";
+ return false; // ----- >>
+ }
using Alpha_value_iterator = typename std::vector<FT>::const_iterator;
Alpha_value_iterator alpha_value_iterator = alpha_values.begin();
@@ -560,8 +551,10 @@ Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Bare_
std::clog << "cells \t\t" << count_cells << std::endl;
#endif // DEBUG_TRACES
// --------------------------------------------------------------------------------------------
- // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension
- complex.make_filtration_non_decreasing();
+ if (Complexity == complexity::FAST)
+ // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension
+ // Only in FAST version, cf. https://github.com/GUDHI/gudhi-devel/issues/57
+ complex.make_filtration_non_decreasing();
// Remove all simplices that have a filtration value greater than max_alpha_square
complex.prune_above_filtration(max_alpha_square);
// --------------------------------------------------------------------------------------------
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-04 17:48:58 +0000