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diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
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+/* 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) 2016 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "rips_complex"
+#include <boost/test/unit_test.hpp>
+
+#include <cmath> // float comparison
+#include <limits>
+#include <string>
+#include <vector>
+#include <algorithm> // std::max
+
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Sparse_rips_complex.h>
+// to construct Rips_complex from a OFF file of points
+#include <gudhi/Points_off_io.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/reader_utils.h>
+#include <gudhi/Unitary_tests_utils.h>
+
+// Type definitions
+using Point = std::vector<double>;
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>;
+using Sparse_rips_complex = Gudhi::rips_complex::Sparse_rips_complex<Simplex_tree::Filtration_value>;
+using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
+ // ----------------------------------------------------------------------------
+ //
+ // Init of a Rips complex from a OFF file
+ //
+ // ----------------------------------------------------------------------------
+ std::string off_file_name("alphacomplexdoc.off");
+ double rips_threshold = 12.0;
+ std::cout << "========== OFF FILE NAME = " << off_file_name << " - Rips threshold=" <<
+ rips_threshold << "==========" << std::endl;
+
+ Gudhi::Points_off_reader<Point> off_reader(off_file_name);
+ Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Gudhi::Euclidean_distance());
+
+ const int DIMENSION_1 = 1;
+ Simplex_tree st;
+ rips_complex_from_file.create_complex(st, DIMENSION_1);
+ std::cout << "st.dimension()=" << st.dimension() << std::endl;
+ BOOST_CHECK(st.dimension() == DIMENSION_1);
+
+ const int NUMBER_OF_VERTICES = 7;
+ std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+ BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES);
+
+ std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+ BOOST_CHECK(st.num_simplices() == 18);
+
+ // Check filtration values of vertices is 0.0
+ for (auto f_simplex : st.skeleton_simplex_range(0)) {
+ BOOST_CHECK(st.filtration(f_simplex) == 0.0);
+ }
+
+ // Check filtration values of edges
+ for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) {
+ if (DIMENSION_1 == st.dimension(f_simplex)) {
+ std::vector<Point> vp;
+ std::cout << "vertex = (";
+ for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+ std::cout << vertex << ",";
+ vp.push_back(off_reader.get_point_cloud().at(vertex));
+ }
+ std::cout << ") - distance =" << Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)) <<
+ " - filtration =" << st.filtration(f_simplex) << std::endl;
+ BOOST_CHECK(vp.size() == 2);
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)));
+ }
+ }
+
+ const int DIMENSION_2 = 2;
+ Simplex_tree st2;
+ rips_complex_from_file.create_complex(st2, DIMENSION_2);
+ std::cout << "st2.dimension()=" << st2.dimension() << std::endl;
+ BOOST_CHECK(st2.dimension() == DIMENSION_2);
+
+ std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl;
+ BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES);
+
+ std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl;
+ BOOST_CHECK(st2.num_simplices() == 23);
+
+ Simplex_tree::Filtration_value f01 = st2.filtration(st2.find({0, 1}));
+ Simplex_tree::Filtration_value f02 = st2.filtration(st2.find({0, 2}));
+ Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2}));
+ Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
+ std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl;
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::max(f01, std::max(f02,f12)));
+
+ Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5}));
+ Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6}));
+ Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6}));
+ Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6}));
+ std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl;
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f456, std::max(f45, std::max(f56,f46)));
+
+ const int DIMENSION_3 = 3;
+ Simplex_tree st3;
+ rips_complex_from_file.create_complex(st3, DIMENSION_3);
+ std::cout << "st3.dimension()=" << st3.dimension() << std::endl;
+ BOOST_CHECK(st3.dimension() == DIMENSION_3);
+
+ std::cout << "st3.num_vertices()=" << st3.num_vertices() << std::endl;
+ BOOST_CHECK(st3.num_vertices() == NUMBER_OF_VERTICES);
+
+ std::cout << "st3.num_simplices()=" << st3.num_simplices() << std::endl;
+ BOOST_CHECK(st3.num_simplices() == 24);
+
+ Simplex_tree::Filtration_value f123 = st3.filtration(st3.find({1, 2, 3}));
+ Simplex_tree::Filtration_value f013 = st3.filtration(st3.find({0, 1, 3}));
+ Simplex_tree::Filtration_value f023 = st3.filtration(st3.find({0, 2, 3}));
+ Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3}));
+ std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 <<
+ " - f023= " << f023 << std::endl;
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f0123, std::max(f012, std::max(f123, std::max(f013, f023))));
+
+}
+
+using Vector_of_points = std::vector<Point>;
+
+bool is_point_in_list(Vector_of_points points_list, Point point) {
+ for (auto& point_in_list : points_list) {
+ if (point_in_list == point) {
+ return true; // point found
+ }
+ }
+ return false; // point not found
+}
+
+class Custom_square_euclidean_distance {
+ public:
+ template< typename Point >
+ auto operator()(const Point& p1, const Point& p2) -> typename Point::value_type {
+ auto it1 = p1.begin();
+ auto it2 = p2.begin();
+ typename Point::value_type dist = 0.;
+ for (; it1 != p1.end(); ++it1, ++it2) {
+ typename Point::value_type tmp = (*it1) - (*it2);
+ dist += tmp*tmp;
+ }
+ return dist;
+ }
+};
+
+BOOST_AUTO_TEST_CASE(Rips_complex_from_points) {
+ // ----------------------------------------------------------------------------
+ // Init of a list of points
+ // ----------------------------------------------------------------------------
+ Vector_of_points points;
+ std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
+ points.push_back(Point(coords.begin(), coords.end()));
+ coords = { 0.0, 0.0, 1.0, 0.0 };
+ points.push_back(Point(coords.begin(), coords.end()));
+ coords = { 0.0, 1.0, 0.0, 0.0 };
+ points.push_back(Point(coords.begin(), coords.end()));
+ coords = { 1.0, 0.0, 0.0, 0.0 };
+ points.push_back(Point(coords.begin(), coords.end()));
+
+ // ----------------------------------------------------------------------------
+ // Init of a Rips complex from the list of points
+ // ----------------------------------------------------------------------------
+ Rips_complex rips_complex_from_points(points, 2.0, Custom_square_euclidean_distance());
+
+ std::cout << "========== Rips_complex_from_points ==========" << std::endl;
+ Simplex_tree st;
+ const int DIMENSION = 3;
+ rips_complex_from_points.create_complex(st, DIMENSION);
+
+ // Another way to check num_simplices
+ std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" << std::endl;
+ int num_simplices = 0;
+ for (auto f_simplex : st.filtration_simplex_range()) {
+ num_simplices++;
+ std::cout << " ( ";
+ for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+ std::cout << vertex << " ";
+ }
+ std::cout << ") -> " << "[" << st.filtration(f_simplex) << "] ";
+ std::cout << std::endl;
+ }
+ BOOST_CHECK(num_simplices == 15);
+ std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+ BOOST_CHECK(st.num_simplices() == 15);
+
+ std::cout << "st.dimension()=" << st.dimension() << std::endl;
+ BOOST_CHECK(st.dimension() == DIMENSION);
+ std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+ BOOST_CHECK(st.num_vertices() == 4);
+
+ for (auto f_simplex : st.filtration_simplex_range()) {
+ std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl;
+ switch (st.dimension(f_simplex)) {
+ case 0:
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0);
+ break;
+ case 1:
+ case 2:
+ case 3:
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 2.0);
+ break;
+ default:
+ BOOST_CHECK(false); // Shall not happen
+ break;
+ }
+ }
+}
+
+BOOST_AUTO_TEST_CASE(Sparse_rips_complex_from_points) {
+ // This is a clone of the test above
+ // ----------------------------------------------------------------------------
+ // Init of a list of points
+ // ----------------------------------------------------------------------------
+ Vector_of_points points;
+ std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
+ points.push_back(Point(coords.begin(), coords.end()));
+ coords = { 0.0, 0.0, 1.0, 0.0 };
+ points.push_back(Point(coords.begin(), coords.end()));
+ coords = { 0.0, 1.0, 0.0, 0.0 };
+ points.push_back(Point(coords.begin(), coords.end()));
+ coords = { 1.0, 0.0, 0.0, 0.0 };
+ points.push_back(Point(coords.begin(), coords.end()));
+
+ // ----------------------------------------------------------------------------
+ // Init of a Rips complex from the list of points
+ // ----------------------------------------------------------------------------
+ // .001 is small enough that we get a deterministic result matching the exact Rips
+ Sparse_rips_complex sparse_rips(points, Custom_square_euclidean_distance(), .001);
+
+ std::cout << "========== Sparse_rips_complex_from_points ==========" << std::endl;
+ Simplex_tree st;
+ const int DIMENSION = 3;
+ sparse_rips.create_complex(st, DIMENSION);
+
+ // Another way to check num_simplices
+ std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" << std::endl;
+ int num_simplices = 0;
+ for (auto f_simplex : st.filtration_simplex_range()) {
+ num_simplices++;
+ std::cout << " ( ";
+ for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+ std::cout << vertex << " ";
+ }
+ std::cout << ") -> " << "[" << st.filtration(f_simplex) << "] ";
+ std::cout << std::endl;
+ }
+ BOOST_CHECK(num_simplices == 15);
+ std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+ BOOST_CHECK(st.num_simplices() == 15);
+
+ std::cout << "st.dimension()=" << st.dimension() << std::endl;
+ BOOST_CHECK(st.dimension() == DIMENSION);
+ std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+ BOOST_CHECK(st.num_vertices() == 4);
+
+ for (auto f_simplex : st.filtration_simplex_range()) {
+ std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl;
+ switch (st.dimension(f_simplex)) {
+ case 0:
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0);
+ break;
+ case 1:
+ case 2:
+ case 3:
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 2.0);
+ break;
+ default:
+ BOOST_CHECK(false); // Shall not happen
+ break;
+ }
+ }
+}
+
+BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
+ // ----------------------------------------------------------------------------
+ //
+ // Init of a Rips complex from a OFF file
+ //
+ // ----------------------------------------------------------------------------
+ std::string csv_file_name("full_square_distance_matrix.csv");
+ double rips_threshold = 12.0;
+ std::cout << "========== CSV FILE NAME = " << csv_file_name << " - Rips threshold=" <<
+ rips_threshold << "==========" << std::endl;
+
+ Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+ Rips_complex rips_complex_from_file(distances, rips_threshold);
+
+ const int DIMENSION_1 = 1;
+ Simplex_tree st;
+ rips_complex_from_file.create_complex(st, DIMENSION_1);
+ std::cout << "st.dimension()=" << st.dimension() << std::endl;
+ BOOST_CHECK(st.dimension() == DIMENSION_1);
+
+ const int NUMBER_OF_VERTICES = 7;
+ std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+ BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES);
+
+ std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+ BOOST_CHECK(st.num_simplices() == 18);
+
+ // Check filtration values of vertices is 0.0
+ for (auto f_simplex : st.skeleton_simplex_range(0)) {
+ BOOST_CHECK(st.filtration(f_simplex) == 0.0);
+ }
+
+ // Check filtration values of edges
+ for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) {
+ if (DIMENSION_1 == st.dimension(f_simplex)) {
+ std::vector<Simplex_tree::Vertex_handle> vvh;
+ std::cout << "vertex = (";
+ for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+ std::cout << vertex << ",";
+ vvh.push_back(vertex);
+ }
+ std::cout << ") - filtration =" << st.filtration(f_simplex) << std::endl;
+ BOOST_CHECK(vvh.size() == 2);
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)]);
+ }
+ }
+
+ const int DIMENSION_2 = 2;
+ Simplex_tree st2;
+ rips_complex_from_file.create_complex(st2, DIMENSION_2);
+ std::cout << "st2.dimension()=" << st2.dimension() << std::endl;
+ BOOST_CHECK(st2.dimension() == DIMENSION_2);
+
+ std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl;
+ BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES);
+
+ std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl;
+ BOOST_CHECK(st2.num_simplices() == 23);
+
+ Simplex_tree::Filtration_value f01 = st2.filtration(st2.find({0, 1}));
+ Simplex_tree::Filtration_value f02 = st2.filtration(st2.find({0, 2}));
+ Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2}));
+ Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
+ std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl;
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::max(f01, std::max(f02,f12)));
+
+ Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5}));
+ Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6}));
+ Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6}));
+ Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6}));
+ std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl;
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f456, std::max(f45, std::max(f56,f46)));
+
+ const int DIMENSION_3 = 3;
+ Simplex_tree st3;
+ rips_complex_from_file.create_complex(st3, DIMENSION_3);
+ std::cout << "st3.dimension()=" << st3.dimension() << std::endl;
+ BOOST_CHECK(st3.dimension() == DIMENSION_3);
+
+ std::cout << "st3.num_vertices()=" << st3.num_vertices() << std::endl;
+ BOOST_CHECK(st3.num_vertices() == NUMBER_OF_VERTICES);
+
+ std::cout << "st3.num_simplices()=" << st3.num_simplices() << std::endl;
+ BOOST_CHECK(st3.num_simplices() == 24);
+
+ Simplex_tree::Filtration_value f123 = st3.filtration(st3.find({1, 2, 3}));
+ Simplex_tree::Filtration_value f013 = st3.filtration(st3.find({0, 1, 3}));
+ Simplex_tree::Filtration_value f023 = st3.filtration(st3.find({0, 2, 3}));
+ Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3}));
+ std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 <<
+ " - f023= " << f023 << std::endl;
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f0123, std::max(f012, std::max(f123, std::max(f013, f023))));
+
+}
+
+#ifdef GUDHI_DEBUG
+BOOST_AUTO_TEST_CASE(Rips_create_complex_throw) {
+ // ----------------------------------------------------------------------------
+ //
+ // Init of a Rips complex from a OFF file
+ //
+ // ----------------------------------------------------------------------------
+ std::string off_file_name("alphacomplexdoc.off");
+ double rips_threshold = 12.0;
+ std::cout << "========== OFF FILE NAME = " << off_file_name << " - Rips threshold=" <<
+ rips_threshold << "==========" << std::endl;
+
+ Gudhi::Points_off_reader<Point> off_reader(off_file_name);
+ Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Gudhi::Euclidean_distance());
+
+ Simplex_tree stree;
+ std::vector<int> simplex = {0, 1, 2};
+ stree.insert_simplex_and_subfaces(simplex);
+ std::cout << "Check exception throw in debug mode" << std::endl;
+ // throw excpt because stree is not empty
+ BOOST_CHECK_THROW (rips_complex_from_file.create_complex(stree, 1), std::invalid_argument);
+}
+#endif
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