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authorvrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2018-06-22 08:30:53 +0000
committervrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2018-06-22 08:30:53 +0000
commit138ee2657f03206209ff5c7d6c4392168beef819 (patch)
tree62f464875d12d48c2eb79a14def1dda8383849a7 /src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
parent82f15e71f43a5547627699b625830126dad1c4ab (diff)
Use unique_ptr to store cgal alpha_shapes_3. Required for not objects_ to be freed.
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3626 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6dc9bbe25757a1a7bef2178ef63876c20d3a38b1
Diffstat (limited to 'src/Alpha_complex/include/gudhi/Alpha_complex_3d.h')
-rw-r--r--src/Alpha_complex/include/gudhi/Alpha_complex_3d.h294
1 files changed, 138 insertions, 156 deletions
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
index 79f8593d..c8bc9c8e 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
@@ -37,6 +37,12 @@
#include <CGAL/tuple.h>
#include <CGAL/iterator.h>
+#include <iostream>
+#include <vector>
+#include <map>
+#include <stdexcept>
+#include <cstddef>
+#include <memory> // for std::unique_ptr
namespace Gudhi {
@@ -44,19 +50,17 @@ namespace alpha_complex {
template<typename AlphaComplex3dOptions>
class Alpha_complex_3d {
-private:
using Alpha_shape_3 = typename AlphaComplex3dOptions::Alpha_shape_3;
- // filtration with alpha values needed type definition
using Alpha_value_type = typename Alpha_shape_3::FT;
- using Object = CGAL::Object;
- using Dispatch = CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
- CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
- std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
+ using Dispatch =
+ CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<CGAL::Object, Alpha_value_type>,
+ CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<CGAL::Object> >,
+ std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
+
using Cell_handle = typename Alpha_shape_3::Cell_handle;
using Facet = typename Alpha_shape_3::Facet;
- using Edge_3 = typename Alpha_shape_3::Edge;
+ using Edge = typename Alpha_shape_3::Edge;
using Alpha_vertex_handle = typename Alpha_shape_3::Vertex_handle;
-
#if BOOST_VERSION >= 105400
using Vertex_list = boost::container::static_vector<Alpha_vertex_handle, 4>;
#else
@@ -64,6 +68,9 @@ private:
#endif
public:
+ using Point_3 = typename AlphaComplex3dOptions::Point_3;
+
+public:
/** \brief Alpha_complex constructor from a list of points.
*
* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous.
@@ -75,17 +82,19 @@ public:
*/
template<typename InputPointRange >
Alpha_complex_3d(const InputPointRange& points) {
- static_assert(!AlphaComplex3dOptions::weighted, "This constructor is not available for weighted versions of Alpha_complex_3d");
- static_assert(!AlphaComplex3dOptions::periodic, "This constructor is not available for periodic versions of Alpha_complex_3d");
- std::cout << points[0] << std::endl;
- Alpha_shape_3 alpha_shape_3(std::begin(points), std::end(points), 0, Alpha_shape_3::GENERAL);
+ static_assert(!AlphaComplex3dOptions::weighted,
+ "This constructor is not available for weighted versions of Alpha_complex_3d");
+ static_assert(!AlphaComplex3dOptions::periodic,
+ "This constructor is not available for periodic versions of Alpha_complex_3d");
- Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
- std::back_inserter(the_alpha_values));
+ alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(new Alpha_shape_3(points.begin(), points.end(), 0,
+ Alpha_shape_3::GENERAL));
+ Dispatch dispatcher = CGAL::dispatch_output<CGAL::Object, Alpha_value_type>(std::back_inserter(objects_),
+ std::back_inserter(alpha_values_));
- alpha_shape_3.filtration_with_alpha_values(disp);
+ alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher);
#ifdef DEBUG_TRACES
- std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+ std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl;
#endif // DEBUG_TRACES
}
@@ -106,7 +115,7 @@ public:
static_assert(!AlphaComplex3dOptions::periodic,
"This constructor is not available for periodic versions of Alpha_complex_3d");
GUDHI_CHECK((weights.size() == points.size()),
- std::invalid_argument("Alpha_complex_3d constructor with weights requires points number to be equal with points number"));
+ std::invalid_argument("Points number in range different from weights range number"));
using Weighted_point_3 = typename AlphaComplex3dOptions::Weighted_point_3;
std::vector<Weighted_point_3> weighted_points_3;
@@ -118,14 +127,17 @@ public:
index++;
}
- Alpha_shape_3 alpha_shape_3(std::begin(weighted_points_3), std::end(weighted_points_3), 0, Alpha_shape_3::GENERAL);
+ 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));
- Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
- std::back_inserter(the_alpha_values));
+ Dispatch dispatcher = CGAL::dispatch_output<CGAL::Object, Alpha_value_type>(std::back_inserter(objects_),
+ std::back_inserter(alpha_values_));
- alpha_shape_3.filtration_with_alpha_values(disp);
+ alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher);
#ifdef DEBUG_TRACES
- std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+ std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl;
#endif // DEBUG_TRACES
}
@@ -140,14 +152,16 @@ public:
*/
template<typename InputPointRange>
Alpha_complex_3d(const InputPointRange& points,
- Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min,
- Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) {
+ double x_min, double y_min, double z_min,
+ double x_max, double y_max, double z_max) {
static_assert(!AlphaComplex3dOptions::weighted,
"This constructor is not available for weighted versions of Alpha_complex_3d");
static_assert(AlphaComplex3dOptions::periodic,
"This constructor is not available for non-periodic versions of Alpha_complex_3d");
// 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),
+ 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."));
using Periodic_delaunay_triangulation_3 = typename AlphaComplex3dOptions::Periodic_delaunay_triangulation_3;
@@ -157,23 +171,27 @@ public:
// Heuristic for inserting large point sets (if pts is reasonably large)
pdt.insert(std::begin(points), std::end(points), true);
// As pdt won't be modified anymore switch to 1-sheeted cover if possible
- GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(),
- std::invalid_argument("Uable to construct a triangulation within a single periodic domain."));
+ // GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(),
+ // std::invalid_argument("Uable to construct a triangulation within a single periodic domain."));
+ if (pdt.is_triangulation_in_1_sheet()) {
+ pdt.convert_to_1_sheeted_covering();
+ } else {
+ std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl;
+ exit(-1);
+ }
+ std::cout << "Periodic Delaunay computed." << std::endl;
// 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 as(pdt, 0, Alpha_shape_3::GENERAL);
-
- // filtration with alpha values from alpha shape
- std::vector<Object> the_objects;
- std::vector<Alpha_value_type> the_alpha_values;
+ alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(new Alpha_shape_3(pdt, 0,
+ Alpha_shape_3::GENERAL));
- Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
- std::back_inserter(the_alpha_values));
+ Dispatch dispatcher = CGAL::dispatch_output<CGAL::Object, Alpha_value_type>(std::back_inserter(objects_),
+ std::back_inserter(alpha_values_));
- as.filtration_with_alpha_values(disp);
+ alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher);
#ifdef DEBUG_TRACES
- std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+ std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl;
#endif // DEBUG_TRACES
}
@@ -196,12 +214,17 @@ public:
static_assert(AlphaComplex3dOptions::periodic,
"This constructor is not available for non-periodic versions of Alpha_complex_3d");
GUDHI_CHECK((weights.size() == points.size()),
- std::invalid_argument("Alpha_complex_3d constructor with weights requires points number to be equal with points number"));
+ 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),
+ 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."));
+#ifdef GUDHI_DEBUG
+ // Defined in GUDHI_DEBUG to avoid unused variable warning
double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);
+#endif
using Weighted_point_3 = typename AlphaComplex3dOptions::Weighted_point_3;
std::vector<Weighted_point_3> weighted_points_3;
@@ -225,25 +248,25 @@ public:
pdt.insert(std::begin(weighted_points_3), std::end(weighted_points_3), true);
// As pdt won't be modified anymore switch to 1-sheeted cover if possible
GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(),
- std::invalid_argument("Uable to construct a triangulation within a single periodic domain."));
+ std::invalid_argument("Unable to construct a triangulation within a single periodic domain."));
+
+ pdt.convert_to_1_sheeted_covering();
// 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 as(pdt, 0, Alpha_shape_3::GENERAL);
+ alpha_shape_3_ptr_ = std::unique_ptr<Alpha_shape_3>(new Alpha_shape_3(pdt, 0,
+ Alpha_shape_3::GENERAL));
- // filtration with alpha values from alpha shape
- std::vector<Object> the_objects;
- std::vector<Alpha_value_type> the_alpha_values;
+ Dispatch dispatcher = CGAL::dispatch_output<CGAL::Object, Alpha_value_type>(std::back_inserter(objects_),
+ std::back_inserter(alpha_values_));
- Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
- std::back_inserter(the_alpha_values));
-
- as.filtration_with_alpha_values(disp);
+ alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher);
#ifdef DEBUG_TRACES
- std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+ std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl;
#endif // DEBUG_TRACES
}
+
template <typename SimplicialComplexForAlpha3d>
void create_complex(SimplicialComplexForAlpha3d& complex) {
using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value;
@@ -251,68 +274,86 @@ public:
}
/** \brief Inserts all Delaunay triangulation into the simplicial complex.
- * It also computes the filtration values accordingly to the \ref createcomplexalgorithm
- *
- * \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$\infty\f$.
- *
- * @return true if creation succeeds, false otherwise.
- *
- * @pre Delaunay triangulation must be already constructed with dimension strictly greater than 0.
- * @pre The simplicial complex must be empty (no vertices)
- *
- * Initialization can be launched once.
- */
+ * It also computes the filtration values accordingly to the \ref createcomplexalgorithm
+ *
+ * \tparam SimplicialComplexForAlpha3d must meet `SimplicialComplexForAlpha3d` concept.
+ *
+ * @param[in] complex SimplicialComplexForAlpha3d to be created.
+ * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
+ *
+ * @return true if creation succeeds, false otherwise.
+ *
+ * @pre The simplicial complex must be empty (no vertices)
+ *
+ * Initialization can be launched once.
+ */
template <typename SimplicialComplexForAlpha3d>
- void create_complex(SimplicialComplexForAlpha3d& complex,
+ bool create_complex(SimplicialComplexForAlpha3d& complex,
typename SimplicialComplexForAlpha3d::Filtration_value max_alpha_square) {
+ if (complex.num_vertices() > 0) {
+ std::cerr << "Alpha_complex_3d create_complex - complex is not empty\n";
+ return false; // ----- >>
+ }
+
using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value;
- using Vertex_handle = typename SimplicialComplexForAlpha3d::Vertex_handle;
+ using Complex_vertex_handle = typename SimplicialComplexForAlpha3d::Vertex_handle;
+ using Alpha_shape_simplex_tree_map = std::map<Alpha_vertex_handle,
+ Complex_vertex_handle>;
+ using Simplex_tree_vector_vertex = std::vector<Complex_vertex_handle>;
+
#ifdef DEBUG_TRACES
- Alpha_shape_3::size_type count_vertices = 0;
- Alpha_shape_3::size_type count_edges = 0;
- Alpha_shape_3::size_type count_facets = 0;
- Alpha_shape_3::size_type count_cells = 0;
+ std::size_t count_vertices = 0;
+ std::size_t count_edges = 0;
+ std::size_t count_facets = 0;
+ std::size_t count_cells = 0;
#endif // DEBUG_TRACES
- // Loop on objects vector
- Vertex_list vertex_list;
- SimplicialComplexForAlpha3d simplex_tree;
- std::map<Alpha_vertex_handle, Vertex_handle> map_cgal_simplex_tree;
- typename std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- for (auto object_iterator : the_objects) {
+ Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
+ auto the_alpha_value_iterator = alpha_values_.begin();
+ for (auto object_iterator : objects_) {
+ Vertex_list vertex_list;
+
// Retrieve Alpha shape vertex list from object
if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
- vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
+ for (auto i = 0; i < 4; i++) {
#ifdef DEBUG_TRACES
- count_cells++;
+ std::cout << "from cell[" << i << "]=" << (*cell)->vertex(i)->point() << std::endl;
#endif // DEBUG_TRACES
+ vertex_list.push_back((*cell)->vertex(i));
+ }
+ count_cells++;
} else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
- vertex_list = from_facet<Vertex_list, Facet>(*facet);
+ for (auto i = 0; i < 4; i++) {
+ if ((*facet).second != i) {
#ifdef DEBUG_TRACES
- count_facets++;
+ std::cout << "from facet=[" << i << "]" << (*facet).first->vertex(i)->point() << std::endl;
#endif // DEBUG_TRACES
- } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
- vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
+ vertex_list.push_back((*facet).first->vertex(i));
+ }
+ }
+ count_facets++;
+ } else if (const Edge *edge = CGAL::object_cast<Edge>(&object_iterator)) {
+ for (auto i : {(*edge).second, (*edge).third}) {
#ifdef DEBUG_TRACES
- count_edges++;
+ std::cout << "from edge[" << i << "]=" << (*edge).first->vertex(i)->point() << std::endl;
#endif // DEBUG_TRACES
- } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
- vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
-#ifdef DEBUG_TRACES
+ vertex_list.push_back((*edge).first->vertex(i));
+ }
+ count_edges++;
+ } else if (const Alpha_vertex_handle *vertex = CGAL::object_cast<Alpha_vertex_handle>(&object_iterator)) {
count_vertices++;
+#ifdef DEBUG_TRACES
+ std::cout << "from vertex=" << (*vertex)->point() << std::endl;
#endif // DEBUG_TRACES
+ vertex_list.push_back((*vertex));
}
// Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- std::vector<Vertex_handle> the_simplex;
+ Simplex_tree_vector_vertex the_simplex;
for (auto the_alpha_shape_vertex : vertex_list) {
- typename std::map<Alpha_vertex_handle, Vertex_handle>::iterator the_map_iterator =
- map_cgal_simplex_tree.find(the_alpha_shape_vertex);
+ auto the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
if (the_map_iterator == map_cgal_simplex_tree.end()) {
// alpha shape not found
- Vertex_handle vertex = map_cgal_simplex_tree.size();
+ Complex_vertex_handle vertex = map_cgal_simplex_tree.size();
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
#endif // DEBUG_TRACES
@@ -320,7 +361,7 @@ public:
map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
} else {
// alpha shape found
- Vertex_handle vertex = the_map_iterator->second;
+ Complex_vertex_handle vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
#endif // DEBUG_TRACES
@@ -332,84 +373,25 @@ public:
#ifdef DEBUG_TRACES
std::cout << "filtration = " << filtr << std::endl;
#endif // DEBUG_TRACES
- simplex_tree.insert_simplex(the_simplex, filtr);
- GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values");
+ complex.insert_simplex(the_simplex, filtr);
+ GUDHI_CHECK(the_alpha_value_iterator != alpha_values_.end(), "CGAL provided more simplices than values");
++the_alpha_value_iterator;
}
#ifdef DEBUG_TRACES
- std::cout << "vertices \t\t" << count_vertices << std::endl;
+ std::cout << "vertices \t" << count_vertices << std::endl;
std::cout << "edges \t\t" << count_edges << std::endl;
std::cout << "facets \t\t" << count_facets << std::endl;
std::cout << "cells \t\t" << count_cells << std::endl;
-
- std::cout << "Information of the Simplex Tree: " << std::endl;
- std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " ";
- std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
- std::cout << " Dimension = " << simplex_tree.dimension() << " ";
-#endif // DEBUG_TRACES
-
-#ifdef DEBUG_TRACES
- std::cout << "Iterator on vertices: " << std::endl;
- for (auto vertex : simplex_tree.complex_vertex_range()) {
- std::cout << vertex << " ";
- }
-#endif // DEBUG_TRACES
-
- }
-
-private:
- template <class Vertex_list, class Cell_handle>
- Vertex_list from_cell(const Cell_handle& ch) {
- Vertex_list the_list;
- for (auto i = 0; i < 4; i++) {
-#ifdef DEBUG_TRACES
- std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
- the_list.push_back(ch->vertex(i));
- }
- return the_list;
- }
-
- template <class Vertex_list, class Facet>
- Vertex_list from_facet(const Facet& fct) {
- Vertex_list the_list;
- for (auto i = 0; i < 4; i++) {
- if (fct.second != i) {
-#ifdef DEBUG_TRACES
- std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
- the_list.push_back(fct.first->vertex(i));
- }
- }
- return the_list;
- }
-
- template <class Vertex_list, class Edge_3>
- Vertex_list from_edge(const Edge_3& edg) {
- Vertex_list the_list;
- for (auto i : {edg.second, edg.third}) {
-#ifdef DEBUG_TRACES
- std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
- the_list.push_back(edg.first->vertex(i));
- }
- return the_list;
- }
-
- template <class Vertex_list, class Vertex_handle>
- Vertex_list from_vertex(const Vertex_handle& vh) {
- Vertex_list the_list;
-#ifdef DEBUG_TRACES
- std::cout << "from vertex=" << vh->point() << std::endl;
#endif // DEBUG_TRACES
- the_list.push_back(vh);
- return the_list;
+ return true;
}
private:
- std::vector<Object> the_objects;
- std::vector<Alpha_value_type> the_alpha_values;
+ // Needs to store alpha_shape_3_ptr_ as objects_ and alpha_shape_3_ptr_ are freed with alpha_shape_3_ptr_
+ std::unique_ptr<Alpha_shape_3> alpha_shape_3_ptr_;
+ std::vector<CGAL::Object> objects_;
+ std::vector<Alpha_value_type> alpha_values_;
};