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-rw-r--r--src/Cech_complex/example/CMakeLists.txt19
-rw-r--r--src/Cech_complex/example/cech_complex_example_from_points.cpp43
-rw-r--r--src/Cech_complex/example/cech_complex_step_by_step.cpp154
3 files changed, 29 insertions, 187 deletions
diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt
index ab391215..7d52ed5e 100644
--- a/src/Cech_complex/example/CMakeLists.txt
+++ b/src/Cech_complex/example/CMakeLists.txt
@@ -1,16 +1,9 @@
-cmake_minimum_required(VERSION 2.6)
project(Cech_complex_examples)
-add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp )
-target_link_libraries(Cech_complex_example_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
-if (TBB_FOUND)
- target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.0.1)
+ add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp)
+ if (TBB_FOUND)
+ target_link_libraries(Cech_complex_example_from_points ${TBB_LIBRARIES})
+ endif()
+ add_test(NAME Cech_complex_example_from_points COMMAND $<TARGET_FILE:Cech_complex_example_from_points>)
endif()
-add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:Cech_complex_example_step_by_step>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-d" "3")
-
-add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp)
-if (TBB_FOUND)
- target_link_libraries(Cech_complex_example_from_points ${TBB_LIBRARIES})
-endif()
-add_test(NAME Cech_complex_example_from_points COMMAND $<TARGET_FILE:Cech_complex_example_from_points>)
diff --git a/src/Cech_complex/example/cech_complex_example_from_points.cpp b/src/Cech_complex/example/cech_complex_example_from_points.cpp
index 3cc5a4df..ef9071ec 100644
--- a/src/Cech_complex/example/cech_complex_example_from_points.cpp
+++ b/src/Cech_complex/example/cech_complex_example_from_points.cpp
@@ -1,30 +1,33 @@
#include <gudhi/Cech_complex.h>
#include <gudhi/Simplex_tree.h>
+#include <CGAL/Epeck_d.h> // For EXACT or SAFE version
+
#include <iostream>
#include <string>
#include <vector>
-#include <array>
int main() {
// Type definitions
- using Point_cloud = std::vector<std::array<double, 2>>;
using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = Simplex_tree::Filtration_value;
- using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>;
+ using Kernel = CGAL::Epeck_d<CGAL::Dimension_tag<2>>;
+ using Point = typename Kernel::Point_d;
+ using Point_cloud = std::vector<Point>;
+ using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>;
Point_cloud points;
- points.push_back({1., 0.}); // 0
- points.push_back({0., 1.}); // 1
- points.push_back({2., 1.}); // 2
- points.push_back({3., 2.}); // 3
- points.push_back({0., 3.}); // 4
- points.push_back({3. + std::sqrt(3.), 3.}); // 5
- points.push_back({1., 4.}); // 6
- points.push_back({3., 4.}); // 7
- points.push_back({2., 4. + std::sqrt(3.)}); // 8
- points.push_back({0., 4.}); // 9
- points.push_back({-0.5, 2.}); // 10
+ points.emplace_back(1., 0.); // 0
+ points.emplace_back(0., 1.); // 1
+ points.emplace_back(2., 1.); // 2
+ points.emplace_back(3., 2.); // 3
+ points.emplace_back(0., 3.); // 4
+ points.emplace_back(3. + std::sqrt(3.), 3.); // 5
+ points.emplace_back(1., 4.); // 6
+ points.emplace_back(3., 4.); // 7
+ points.emplace_back(2., 4. + std::sqrt(3.)); // 8
+ points.emplace_back(0., 4.); // 9
+ points.emplace_back(-0.5, 2.); // 10
// ----------------------------------------------------------------------------
// Init of a Cech complex from points
@@ -37,18 +40,18 @@ int main() {
// ----------------------------------------------------------------------------
// Display information about the one skeleton Cech complex
// ----------------------------------------------------------------------------
- std::cout << "Cech complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - "
+ std::clog << "Cech complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - "
<< stree.num_vertices() << " vertices." << std::endl;
- std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl;
+ std::clog << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl;
for (auto f_simplex : stree.filtration_simplex_range()) {
- std::cout << " ( ";
+ std::clog << " ( ";
for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
- std::cout << vertex << " ";
+ std::clog << vertex << " ";
}
- std::cout << ") -> "
+ std::clog << ") -> "
<< "[" << stree.filtration(f_simplex) << "] ";
- std::cout << std::endl;
+ std::clog << std::endl;
}
return 0;
}
diff --git a/src/Cech_complex/example/cech_complex_step_by_step.cpp b/src/Cech_complex/example/cech_complex_step_by_step.cpp
deleted file mode 100644
index b3d05697..00000000
--- a/src/Cech_complex/example/cech_complex_step_by_step.cpp
+++ /dev/null
@@ -1,154 +0,0 @@
-/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
- * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
- * Author(s): Vincent Rouvreau
- *
- * Copyright (C) 2018 Inria
- *
- * Modification(s):
- * - YYYY/MM Author: Description of the modification
- */
-
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Points_off_io.h>
-
-#include <gudhi/Miniball.hpp>
-
-#include <boost/program_options.hpp>
-
-#include <string>
-#include <vector>
-#include <limits> // infinity
-#include <utility> // for pair
-#include <map>
-
-// ----------------------------------------------------------------------------
-// rips_persistence_step_by_step is an example of each step that is required to
-// build a Rips over a Simplex_tree. Please refer to rips_persistence to see
-// how to do the same thing with the Rips_complex wrapper for less detailed
-// steps.
-// ----------------------------------------------------------------------------
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<>;
-using Simplex_handle = Simplex_tree::Simplex_handle;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Point = std::vector<double>;
-using Points_off_reader = Gudhi::Points_off_reader<Point>;
-using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>;
-
-class Cech_blocker {
- private:
- using Point_cloud = std::vector<Point>;
- using Point_iterator = Point_cloud::const_iterator;
- using Coordinate_iterator = Point::const_iterator;
- using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>;
-
- public:
- bool operator()(Simplex_handle sh) {
- std::vector<Point> points;
- for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) {
- points.push_back(point_cloud_[vertex]);
-#ifdef DEBUG_TRACES
- std::cout << "#(" << vertex << ")#";
-#endif // DEBUG_TRACES
- }
- Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points);
-#ifdef DEBUG_TRACES
- std::cout << "radius = " << radius << " - " << (radius > max_radius_) << std::endl;
-#endif // DEBUG_TRACES
- simplex_tree_.assign_filtration(sh, radius);
- return (radius > max_radius_);
- }
- Cech_blocker(Simplex_tree& simplex_tree, Filtration_value max_radius, const std::vector<Point>& point_cloud)
- : simplex_tree_(simplex_tree), max_radius_(max_radius), point_cloud_(point_cloud) {
- dimension_ = point_cloud_[0].size();
- }
-
- private:
- Simplex_tree simplex_tree_;
- Filtration_value max_radius_;
- std::vector<Point> point_cloud_;
- int dimension_;
-};
-
-void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max);
-
-int main(int argc, char* argv[]) {
- std::string off_file_points;
- Filtration_value max_radius;
- int dim_max;
-
- program_options(argc, argv, off_file_points, max_radius, dim_max);
-
- // Extract the points from the file filepoints
- Points_off_reader off_reader(off_file_points);
-
- // Compute the proximity graph of the points
- Proximity_graph prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(off_reader.get_point_cloud(), max_radius,
- Gudhi::Minimal_enclosing_ball_radius());
-
- // Construct the Rips complex in a Simplex Tree
- Simplex_tree st;
- // insert the proximity graph in the simplex tree
- st.insert_graph(prox_graph);
- // expand the graph until dimension dim_max
- st.expansion_with_blockers(dim_max, Cech_blocker(st, max_radius, off_reader.get_point_cloud()));
-
- std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
- std::cout << " and has dimension " << st.dimension() << " \n";
-
- // Sort the simplices in the order of the filtration
- st.initialize_filtration();
-
-#if DEBUG_TRACES
- std::cout << "********************************************************************\n";
- std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n";
- std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
- for (auto f_simplex : st.filtration_simplex_range()) {
- std::cout << " "
- << "[" << st.filtration(f_simplex) << "] ";
- for (auto vertex : st.simplex_vertex_range(f_simplex)) {
- std::cout << static_cast<int>(vertex) << " ";
- }
- std::cout << std::endl;
- }
-#endif // DEBUG_TRACES
-
- return 0;
-}
-
-void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max) {
- namespace po = boost::program_options;
- po::options_description hidden("Hidden options");
- hidden.add_options()("input-file", po::value<std::string>(&off_file_points),
- "Name of an OFF file containing a point set.\n");
-
- po::options_description visible("Allowed options", 100);
- visible.add_options()("help,h", "produce help message")(
- "max-radius,r",
- po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()),
- "Maximal length of an edge for the Rips complex construction.")(
- "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
- "Maximal dimension of the Rips complex we want to compute.");
-
- po::positional_options_description pos;
- pos.add("input-file", 1);
-
- po::options_description all;
- all.add(visible).add(hidden);
-
- po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
- po::notify(vm);
-
- if (vm.count("help") || !vm.count("input-file")) {
- std::cout << std::endl;
- std::cout << "Construct a Cech complex defined on a set of input points.\n \n";
-
- std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
- std::cout << visible << std::endl;
- exit(-1);
- }
-}
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