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-rw-r--r--src/Alpha_complex/include/gudhi/Alpha_complex.h142
1 files changed, 75 insertions, 67 deletions
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index f2a05e95..1b5d6997 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -237,7 +237,7 @@ class Alpha_complex {
for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) {
if (!triangulation_->is_infinite(*vit)) {
#ifdef DEBUG_TRACES
- std::cout << "Vertex insertion - " << vit->data() << " -> " << vit->point() << std::endl;
+ std::clog << "Vertex insertion - " << vit->data() << " -> " << vit->point() << std::endl;
#endif // DEBUG_TRACES
vertex_handle_to_iterator_[vit->data()] = vit;
}
@@ -248,16 +248,21 @@ class Alpha_complex {
public:
/** \brief Inserts all Delaunay triangulation into the simplicial complex.
- * It also computes the filtration values accordingly to the \ref createcomplexalgorithm
+ * It also computes the filtration values accordingly to the \ref createcomplexalgorithm if default_filtration_value
+ * is not set.
*
* \tparam SimplicialComplexForAlpha must meet `SimplicialComplexForAlpha` concept.
*
* @param[in] complex SimplicialComplexForAlpha to be created.
* @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$, and there is very
- * little point using anything else since it does not save time.
+ * little point using anything else since it does not save time. Useless if `default_filtration_value` is set to
+ * `true`.
* @param[in] exact Exact filtration values computation. Not exact if `Kernel` is not <a target="_blank"
* href="https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epeck__d.html">CGAL::Epeck_d</a>.
- *
+ * @param[in] default_filtration_value Set this value to `true` if filtration values are not needed to be computed
+ * (will be set to `NaN`).
+ * Default value is `false` (which means compute the filtration values).
+ *
* @return true if creation succeeds, false otherwise.
*
* @pre Delaunay triangulation must be already constructed with dimension strictly greater than 0.
@@ -269,7 +274,8 @@ class Alpha_complex {
typename Filtration_value = typename SimplicialComplexForAlpha::Filtration_value>
bool create_complex(SimplicialComplexForAlpha& complex,
Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity(),
- bool exact = false) {
+ bool exact = false,
+ bool default_filtration_value = false) {
// From SimplicialComplexForAlpha type required to insert into a simplicial complex (with or without subfaces).
typedef typename SimplicialComplexForAlpha::Vertex_handle Vertex_handle;
typedef typename SimplicialComplexForAlpha::Simplex_handle Simplex_handle;
@@ -296,19 +302,19 @@ class Alpha_complex {
++cit) {
Vector_vertex vertexVector;
#ifdef DEBUG_TRACES
- std::cout << "Simplex_tree insertion ";
+ std::clog << "Simplex_tree insertion ";
#endif // DEBUG_TRACES
for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
if (*vit != nullptr) {
#ifdef DEBUG_TRACES
- std::cout << " " << (*vit)->data();
+ std::clog << " " << (*vit)->data();
#endif // DEBUG_TRACES
// Vector of vertex construction for simplex_tree structure
vertexVector.push_back((*vit)->data());
}
}
#ifdef DEBUG_TRACES
- std::cout << std::endl;
+ std::clog << std::endl;
#endif // DEBUG_TRACES
// Insert each simplex and its subfaces in the simplex tree - filtration is NaN
complex.insert_simplex_and_subfaces(vertexVector, std::numeric_limits<double>::quiet_NaN());
@@ -316,62 +322,64 @@ class Alpha_complex {
}
// --------------------------------------------------------------------------------------------
- // --------------------------------------------------------------------------------------------
- // Will be re-used many times
- Vector_of_CGAL_points pointVector;
- // ### For i : d -> 0
- for (int decr_dim = triangulation_->maximal_dimension(); decr_dim >= 0; decr_dim--) {
- // ### Foreach Sigma of dim i
- for (Simplex_handle f_simplex : complex.skeleton_simplex_range(decr_dim)) {
- int f_simplex_dim = complex.dimension(f_simplex);
- if (decr_dim == f_simplex_dim) {
- pointVector.clear();
-#ifdef DEBUG_TRACES
- std::cout << "Sigma of dim " << decr_dim << " is";
-#endif // DEBUG_TRACES
- for (auto vertex : complex.simplex_vertex_range(f_simplex)) {
- pointVector.push_back(get_point(vertex));
-#ifdef DEBUG_TRACES
- std::cout << " " << vertex;
-#endif // DEBUG_TRACES
- }
-#ifdef DEBUG_TRACES
- std::cout << std::endl;
-#endif // DEBUG_TRACES
- // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma)
- if (std::isnan(complex.filtration(f_simplex))) {
- Filtration_value alpha_complex_filtration = 0.0;
- // No need to compute squared_radius on a single point - alpha is 0.0
- if (f_simplex_dim > 0) {
- // squared_radius function initialization
- Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object();
-
- CGAL::NT_converter<typename Geom_traits::FT, Filtration_value> cv;
- auto sqrad = squared_radius(pointVector.begin(), pointVector.end());
-#if CGAL_VERSION_NR >= 1050000000
- if(exact) CGAL::exact(sqrad);
-#endif
- alpha_complex_filtration = cv(sqrad);
+ if (!default_filtration_value) {
+ // --------------------------------------------------------------------------------------------
+ // Will be re-used many times
+ Vector_of_CGAL_points pointVector;
+ // ### For i : d -> 0
+ for (int decr_dim = triangulation_->maximal_dimension(); decr_dim >= 0; decr_dim--) {
+ // ### Foreach Sigma of dim i
+ for (Simplex_handle f_simplex : complex.skeleton_simplex_range(decr_dim)) {
+ int f_simplex_dim = complex.dimension(f_simplex);
+ if (decr_dim == f_simplex_dim) {
+ pointVector.clear();
+ #ifdef DEBUG_TRACES
+ std::clog << "Sigma of dim " << decr_dim << " is";
+ #endif // DEBUG_TRACES
+ for (auto vertex : complex.simplex_vertex_range(f_simplex)) {
+ pointVector.push_back(get_point(vertex));
+ #ifdef DEBUG_TRACES
+ std::clog << " " << vertex;
+ #endif // DEBUG_TRACES
}
- complex.assign_filtration(f_simplex, alpha_complex_filtration);
-#ifdef DEBUG_TRACES
- std::cout << "filt(Sigma) is NaN : filt(Sigma) =" << complex.filtration(f_simplex) << std::endl;
-#endif // DEBUG_TRACES
+ #ifdef DEBUG_TRACES
+ std::clog << std::endl;
+ #endif // DEBUG_TRACES
+ // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma)
+ if (std::isnan(complex.filtration(f_simplex))) {
+ Filtration_value alpha_complex_filtration = 0.0;
+ // No need to compute squared_radius on a single point - alpha is 0.0
+ if (f_simplex_dim > 0) {
+ // squared_radius function initialization
+ Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object();
+
+ CGAL::NT_converter<typename Geom_traits::FT, Filtration_value> cv;
+ auto sqrad = squared_radius(pointVector.begin(), pointVector.end());
+ #if CGAL_VERSION_NR >= 1050000000
+ if(exact) CGAL::exact(sqrad);
+ #endif
+ alpha_complex_filtration = cv(sqrad);
+ }
+ complex.assign_filtration(f_simplex, alpha_complex_filtration);
+ #ifdef DEBUG_TRACES
+ std::clog << "filt(Sigma) is NaN : filt(Sigma) =" << complex.filtration(f_simplex) << std::endl;
+ #endif // DEBUG_TRACES
+ }
+ // No need to propagate further, unweighted points all have value 0
+ if (decr_dim > 1)
+ propagate_alpha_filtration(complex, f_simplex);
}
- // No need to propagate further, unweighted points all have value 0
- if (decr_dim > 1)
- propagate_alpha_filtration(complex, f_simplex);
}
}
+ // --------------------------------------------------------------------------------------------
+
+ // --------------------------------------------------------------------------------------------
+ // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension
+ 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);
+ // --------------------------------------------------------------------------------------------
}
- // --------------------------------------------------------------------------------------------
-
- // --------------------------------------------------------------------------------------------
- // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension
- 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);
- // --------------------------------------------------------------------------------------------
return true;
}
@@ -387,13 +395,13 @@ class Alpha_complex {
// ### Foreach Tau face of Sigma
for (auto f_boundary : complex.boundary_simplex_range(f_simplex)) {
#ifdef DEBUG_TRACES
- std::cout << " | --------------------------------------------------\n";
- std::cout << " | Tau ";
+ std::clog << " | --------------------------------------------------\n";
+ std::clog << " | Tau ";
for (auto vertex : complex.simplex_vertex_range(f_boundary)) {
- std::cout << vertex << " ";
+ std::clog << vertex << " ";
}
- std::cout << "is a face of Sigma\n";
- std::cout << " | isnan(complex.filtration(Tau)=" << std::isnan(complex.filtration(f_boundary)) << std::endl;
+ std::clog << "is a face of Sigma\n";
+ std::clog << " | isnan(complex.filtration(Tau)=" << std::isnan(complex.filtration(f_boundary)) << std::endl;
#endif // DEBUG_TRACES
// ### If filt(Tau) is not NaN
if (!std::isnan(complex.filtration(f_boundary))) {
@@ -402,7 +410,7 @@ class Alpha_complex {
complex.filtration(f_simplex));
complex.assign_filtration(f_boundary, alpha_complex_filtration);
#ifdef DEBUG_TRACES
- std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << complex.filtration(f_boundary) << std::endl;
+ std::clog << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << complex.filtration(f_boundary) << std::endl;
#endif // DEBUG_TRACES
// ### Else
} else {
@@ -432,7 +440,7 @@ class Alpha_complex {
bool is_gab = is_gabriel(pointVector.begin(), pointVector.end(), point_for_gabriel)
!= CGAL::ON_BOUNDED_SIDE;
#ifdef DEBUG_TRACES
- std::cout << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << vertexForGabriel << std::endl;
+ std::clog << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << vertexForGabriel << std::endl;
#endif // DEBUG_TRACES
// ### If Tau is not Gabriel of Sigma
if (false == is_gab) {
@@ -440,7 +448,7 @@ class Alpha_complex {
Filtration_value alpha_complex_filtration = complex.filtration(f_simplex);
complex.assign_filtration(f_boundary, alpha_complex_filtration);
#ifdef DEBUG_TRACES
- std::cout << " | filt(Tau) = filt(Sigma) = " << complex.filtration(f_boundary) << std::endl;
+ std::clog << " | filt(Tau) = filt(Sigma) = " << complex.filtration(f_boundary) << std::endl;
#endif // DEBUG_TRACES
}
}
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