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-rw-r--r--CMakeLists.txt2
-rw-r--r--src/Persistent_cohomology/example/rips_multifield_persistence.cpp78
-rw-r--r--src/Persistent_cohomology/example/rips_persistence.cpp79
-rw-r--r--src/Rips_complex/concept/Simplicial_complex_for_rips.h53
-rw-r--r--src/Rips_complex/doc/Intro_rips_complex.h104
-rw-r--r--src/Rips_complex/doc/rips_complex_representation.ipe326
-rw-r--r--src/Rips_complex/doc/rips_complex_representation.pngbin0 -> 15677 bytes
-rw-r--r--src/Rips_complex/doc/rips_one_skeleton.ipe326
-rw-r--r--src/Rips_complex/doc/rips_one_skeleton.pngbin0 -> 47651 bytes
-rw-r--r--src/Rips_complex/example/CMakeLists.txt8
-rw-r--r--src/Rips_complex/example/example_rips_complex_from_off_file.cpp71
-rw-r--r--src/Rips_complex/include/gudhi/Rips_complex.h154
-rw-r--r--src/Simplex_tree/include/gudhi/Simplex_tree.h2
-rw-r--r--src/common/include/gudhi/distance_functions.h2
-rw-r--r--src/common/include/gudhi/graph_simplicial_complex.h8
15 files changed, 1117 insertions, 96 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 42a56fdc..89e130f4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -123,6 +123,7 @@ else()
include_directories(src/Contraction/include/)
include_directories(src/Hasse_complex/include/)
include_directories(src/Persistent_cohomology/include/)
+ include_directories(src/Rips_complex/include/)
include_directories(src/Simplex_tree/include/)
include_directories(src/Skeleton_blocker/include/)
include_directories(src/Witness_complex/include/)
@@ -142,6 +143,7 @@ else()
add_subdirectory(src/Bitmap_cubical_complex/example)
add_subdirectory(src/Alpha_complex/example)
add_subdirectory(src/Alpha_complex/test)
+ add_subdirectory(src/Rips_complex/example)
# data points generator
add_subdirectory(data/points/generator)
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index c5cd775d..d4a07bb6 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -20,8 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/reader_utils.h>
-#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Rips_complex.h>
#include <gudhi/distance_functions.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
@@ -32,14 +31,11 @@
#include <string>
#include <vector>
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-typedef int Vertex_handle;
typedef double Filtration_value;
void program_options(int argc, char * argv[]
- , std::string & filepoints
+ , std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
@@ -48,7 +44,7 @@ void program_options(int argc, char * argv[]
, Filtration_value & min_persistence);
int main(int argc, char * argv[]) {
- std::string filepoints;
+ std::string off_file_points;
std::string filediag;
Filtration_value threshold;
int dim_max;
@@ -56,49 +52,43 @@ int main(int argc, char * argv[]) {
int max_p;
Filtration_value min_persistence;
- program_options(argc, argv, filepoints, filediag, threshold, dim_max, min_p, max_p, min_persistence);
+ program_options(argc, argv, off_file_points, filediag, threshold, dim_max, min_p, max_p, min_persistence);
- // Extract the points from the file filepoints
- typedef std::vector<double> Point_t;
- std::vector< Point_t > points;
- read_points(filepoints, points);
-
- // Compute the proximity graph of the points
- Graph_t prox_graph = compute_proximity_graph(points, threshold
- , euclidean_distance<Point_t>);
+ Gudhi::rips_complex::Rips_complex<> rips_complex_from_file(off_file_points);
// Construct the Rips complex in a Simplex Tree
- typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
- ST st;
- // insert the proximity graph in the simplex tree
- st.insert_graph(prox_graph);
- // expand the graph until dimension dim_max
- st.expansion(dim_max);
-
- // Sort the simplices in the order of the filtration
- st.initialize_filtration();
-
- // Compute the persistence diagram of the complex
- Persistent_cohomology<ST, Multi_field > pcoh(st);
- // initializes the coefficient field for homology
- pcoh.init_coefficients(min_p, max_p);
- // compute persistent homology, disgarding persistent features of life shorter than min_persistence
- pcoh.compute_persistent_cohomology(min_persistence);
-
- // Output the diagram in filediag
- if (filediag.empty()) {
- pcoh.output_diagram();
- } else {
- std::ofstream out(filediag);
- pcoh.output_diagram(out);
- out.close();
+ using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+ Simplex_tree simplex_tree;
+
+ if (rips_complex_from_file.create_complex(simplex_tree, threshold, dim_max, euclidean_distance<std::vector<double>>)) {
+ std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+ std::cout << " and has dimension " << simplex_tree.dimension() << " \n";
+
+ // Sort the simplices in the order of the filtration
+ simplex_tree.initialize_filtration();
+
+ using Multi_field = Gudhi::persistent_cohomology::Multi_field;
+ // Compute the persistence diagram of the complex
+ Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Multi_field > pcoh(simplex_tree);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(min_p, max_p);
+
+ pcoh.compute_persistent_cohomology(min_persistence);
+
+ // Output the diagram in filediag
+ if (filediag.empty()) {
+ pcoh.output_diagram();
+ } else {
+ std::ofstream out(filediag);
+ pcoh.output_diagram(out);
+ out.close();
+ }
}
-
return 0;
}
void program_options(int argc, char * argv[]
- , std::string & filepoints
+ , std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
@@ -108,8 +98,8 @@ void program_options(int argc, char * argv[]
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
hidden.add_options()
- ("input-file", po::value<std::string>(&filepoints),
- "Name of file containing a point set. Format is one point per line: X1 ... Xd \n");
+ ("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");
visible.add_options()
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index cab49395..e3ab5927 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -20,7 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <gudhi/reader_utils.h>
+#include <gudhi/Rips_complex.h>
#include <gudhi/graph_simplicial_complex.h>
#include <gudhi/distance_functions.h>
#include <gudhi/Simplex_tree.h>
@@ -32,14 +32,10 @@
#include <vector>
#include <limits> // infinity
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
typedef double Filtration_value;
void program_options(int argc, char * argv[]
- , std::string & filepoints
+ , std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
@@ -47,59 +43,50 @@ void program_options(int argc, char * argv[]
, Filtration_value & min_persistence);
int main(int argc, char * argv[]) {
- std::string filepoints;
+ std::string off_file_points;
std::string filediag;
Filtration_value threshold;
int dim_max;
int p;
Filtration_value min_persistence;
- program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence);
-
- // Extract the points from the file filepoints
- typedef std::vector<double> Point_t;
- std::vector< Point_t > points;
- read_points(filepoints, points);
+ program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
- // Compute the proximity graph of the points
- Graph_t prox_graph = compute_proximity_graph(points, threshold
- , euclidean_distance<Point_t>);
+ Gudhi::rips_complex::Rips_complex<> rips_complex_from_file(off_file_points);
// Construct the Rips complex in a Simplex Tree
- typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
- ST st;
- // insert the proximity graph in the simplex tree
- st.insert_graph(prox_graph);
- // expand the graph until dimension dim_max
- st.expansion(dim_max);
-
- 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();
-
- // Compute the persistence diagram of the complex
- persistent_cohomology::Persistent_cohomology<ST, Field_Zp > pcoh(st);
- // initializes the coefficient field for homology
- pcoh.init_coefficients(p);
-
- pcoh.compute_persistent_cohomology(min_persistence);
-
- // Output the diagram in filediag
- if (filediag.empty()) {
- pcoh.output_diagram();
- } else {
- std::ofstream out(filediag);
- pcoh.output_diagram(out);
- out.close();
+ using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+ Simplex_tree simplex_tree;
+
+ if (rips_complex_from_file.create_complex(simplex_tree, threshold, dim_max, euclidean_distance<std::vector<double>>)) {
+ std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+ std::cout << " and has dimension " << simplex_tree.dimension() << " \n";
+
+ // Sort the simplices in the order of the filtration
+ simplex_tree.initialize_filtration();
+
+ using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+ // Compute the persistence diagram of the complex
+ Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp > pcoh(simplex_tree);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(p);
+
+ pcoh.compute_persistent_cohomology(min_persistence);
+
+ // Output the diagram in filediag
+ if (filediag.empty()) {
+ pcoh.output_diagram();
+ } else {
+ std::ofstream out(filediag);
+ pcoh.output_diagram(out);
+ out.close();
+ }
}
-
return 0;
}
void program_options(int argc, char * argv[]
- , std::string & filepoints
+ , std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
@@ -108,7 +95,7 @@ void program_options(int argc, char * argv[]
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
hidden.add_options()
- ("input-file", po::value<std::string>(&filepoints),
+ ("input-file", po::value<std::string>(&off_file_points),
"Name of file containing a point set. Format is one point per line: X1 ... Xd ");
po::options_description visible("Allowed options", 100);
diff --git a/src/Rips_complex/concept/Simplicial_complex_for_rips.h b/src/Rips_complex/concept/Simplicial_complex_for_rips.h
new file mode 100644
index 00000000..470860e9
--- /dev/null
+++ b/src/Rips_complex/concept/Simplicial_complex_for_rips.h
@@ -0,0 +1,53 @@
+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
+ * library for computational topology.
+ *
+ * Author(s): Vincent Rouvreau
+ *
+ * Copyright (C) 2016 INRIA
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_
+#define CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+/** \brief The concept SimplicialComplexForRips describes the requirements for a type to implement a simplicial
+ * complex, that can be created from a `Rips_complex`.
+ */
+struct SimplicialComplexForRips {
+ /** Handle to specify the simplex filtration value. */
+ typedef unspecified Filtration_value;
+
+ /** Returns the number of vertices in the simplicial complex. */
+ std::size_t num_vertices();
+
+ /** \brief Inserts a a given range 'OneSkeletonGraph' in the simplicial complex. */
+ template<class OneSkeletonGraph>
+ void insert_graph(const OneSkeletonGraph& skel_graph);
+
+ /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension. */
+ void expansion(int max_dim);
+
+};
+
+} // namespace rips_complex
+
+} // namespace Gudhi
+
+#endif // CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_
diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
new file mode 100644
index 00000000..85108168
--- /dev/null
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -0,0 +1,104 @@
+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
+ * library for computational topology.
+ *
+ * Author(s): Clément Maria & Vincent Rouvreau
+ *
+ * Copyright (C) 2015 INRIA
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
+#define DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+/** \defgroup rips_complex Rips complex
+ *
+ * \author Clément Maria & Vincent Rouvreau
+ *
+ * @{
+ *
+ * \section definition Definition
+ *
+ * Rips_complex
+ * <a target="_blank" href="https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex">(Wikipedia)</a> is a
+ * <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a>
+ * constructed from a one skeleton graph.
+ *
+ * The filtration value of each edge is computed from a user-given distance function.
+ *
+ * All edges that have a filtration value strictly greater than a given threshold value are not inserted into
+ * the complex.
+ *
+ * When creating a simplicial complex from this one skeleton graph, rips inserts the one skeleton graph into the data
+ * structure, and then expands the simplicial when required.
+ *
+ * \image html "rips_complex_representation.png" "Rips-complex one skeleton graph representation"
+ *
+ * On this example, as edges (4,5), (4,6) and (5,6) are in the complex, simplex (4,5,6) is added with the filtration
+ * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$.
+ * And so on for simplex (0,1,2,3).
+ *
+ * \section ripspointsexample Example from points
+ *
+ * This example builds the one skeleton graph from the given points, threshold value, and distance function.
+ * Then it creates a `Simplex_tree` with it.
+ *
+ * Then, it is asked to display information about the simplicial complex.
+ *
+ * \include Rips_complex/example_rips_complex_from_points.cpp
+ *
+ * When launching:
+ *
+ * \code $> ./ripspoints
+ * \endcode
+ *
+ * the program output is:
+ *
+ * \include Rips_complex/rips_points_for_doc_12_2.txt
+ *
+ * \section offexample Example from OFF file
+ *
+ * This example builds the one skeleton graph from the given points in an OFF file, threshold value, and distance
+ * function.
+ * Then it creates a `Simplex_tree` with it.
+ *
+ *
+ * Then, it is asked to display information about the rips complex.
+ *
+ * \include Rips_complex/example_rips_complex_from_off_file.cpp
+ *
+ * When launching:
+ *
+ * \code $> ./ripsoffreader ../../data/points/alphacomplexdoc.off 12.0 3
+ * \endcode
+ *
+ * the program output is:
+ *
+ * \include Rips_complex/rips_points_for_doc_12_3.txt
+ *
+ * \copyright GNU General Public License v3.
+ * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ */
+/** @} */ // end defgroup rips_complex
+
+} // namespace rips_complex
+
+} // namespace Gudhi
+
+#endif // DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
diff --git a/src/Rips_complex/doc/rips_complex_representation.ipe b/src/Rips_complex/doc/rips_complex_representation.ipe
new file mode 100644
index 00000000..7f6028f4
--- /dev/null
+++ b/src/Rips_complex/doc/rips_complex_representation.ipe
@@ -0,0 +1,326 @@
+<?xml version="1.0"?>
+<!DOCTYPE ipe SYSTEM "ipe.dtd">
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diff --git a/src/Rips_complex/doc/rips_one_skeleton.png b/src/Rips_complex/doc/rips_one_skeleton.png
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diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
new file mode 100644
index 00000000..6d0deecf
--- /dev/null
+++ b/src/Rips_complex/example/CMakeLists.txt
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+cmake_minimum_required(VERSION 2.6)
+project(Rips_complex_examples)
+
+add_executable ( ripsoffreader example_rips_complex_from_off_file.cpp )
+target_link_libraries(ripsoffreader ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+ target_link_libraries(ripsoffreader ${TBB_LIBRARIES})
+endif()
diff --git a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
new file mode 100644
index 00000000..82baa68e
--- /dev/null
+++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
@@ -0,0 +1,71 @@
+#include <gudhi/Rips_complex.h>
+// to construct Rips_complex from a OFF file of points
+#include <gudhi/Points_off_io.h>
+// to construct a simplex_tree from rips complex
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+
+void usage(int nbArgs, char * const progName) {
+ std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+ std::cerr << "Usage: " << progName << " filename.off threshold dim_max [ouput_file.txt]\n";
+ std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n";
+ exit(-1); // ----- >>
+}
+
+int main(int argc, char **argv) {
+ if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1));
+
+ std::string off_file_name(argv[1]);
+ double threshold = atof(argv[2]);
+ int dim_max = atoi(argv[3]);
+
+ // Type definitions
+ using Point = std::vector<float>;
+ using Simplex_tree = Gudhi::Simplex_tree<>;
+ using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>;
+
+ // ----------------------------------------------------------------------------
+ // Init of a rips complex from an OFF file
+ // ----------------------------------------------------------------------------
+ Gudhi::Points_off_reader<Point> off_reader(off_file_name);
+ Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
+ euclidean_distance<Point>);
+
+ std::streambuf* streambufffer;
+ std::ofstream ouput_file_stream;
+
+ if (argc == 5) {
+ ouput_file_stream.open(std::string(argv[4]));
+ streambufffer = ouput_file_stream.rdbuf();
+ } else {
+ streambufffer = std::cout.rdbuf();
+ }
+
+ Simplex_tree simplex;
+ if (rips_complex_from_file.create_complex(simplex, dim_max)) {
+ std::ostream output_stream(streambufffer);
+
+ // ----------------------------------------------------------------------------
+ // Display information about the rips complex
+ // ----------------------------------------------------------------------------
+ output_stream << "Rips complex is of dimension " << simplex.dimension() <<
+ " - " << simplex.num_simplices() << " simplices - " <<
+ simplex.num_vertices() << " vertices." << std::endl;
+
+ output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+ std::endl;
+ for (auto f_simplex : simplex.filtration_simplex_range()) {
+ output_stream << " ( ";
+ for (auto vertex : simplex.simplex_vertex_range(f_simplex)) {
+ output_stream << vertex << " ";
+ }
+ output_stream << ") -> " << "[" << simplex.filtration(f_simplex) << "] ";
+ output_stream << std::endl;
+ }
+ }
+ ouput_file_stream.close();
+ return 0;
+}
diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h
new file mode 100644
index 00000000..10f674e5
--- /dev/null
+++ b/src/Rips_complex/include/gudhi/Rips_complex.h
@@ -0,0 +1,154 @@
+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
+ * library for computational topology.
+ *
+ * Author(s): Clément Maria & Vincent Rouvreau
+ *
+ * Copyright (C) 2016 INRIA
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef RIPS_COMPLEX_H_
+#define RIPS_COMPLEX_H_
+
+#include <gudhi/Debug_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+
+#include <boost/graph/adjacency_list.hpp>
+
+#include <iostream>
+#include <vector>
+#include <map>
+#include <string>
+#include <limits> // for numeric_limits
+#include <utility> // for pair<>
+
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+/**
+ * \class Rips_complex
+ * \brief Rips complex data structure.
+ *
+ * \ingroup rips_complex
+ *
+ * \details
+ * The data structure is a 1-skeleton graph constructed from a point cloud, containing edges when the edge length is
+ * less or equal to a given threshold. Edge length is computed from a user given function.
+ *
+ * The complex is a template class requiring a Filtration_value type.
+ *
+ * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex.
+ *
+ * \tparam Filtration_value must meet `SimplicialComplexForRips` concept.
+ */
+template<typename Filtration_value>
+class Rips_complex {
+ private:
+ typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+ , boost::property < vertex_filtration_t, Filtration_value >
+ , boost::property < edge_filtration_t, Filtration_value >> Graph_t;
+
+ typedef int Vertex_handle;
+
+ public:
+ /** \brief Rips_complex constructor from a list of points.
+ *
+ * @param[in] points Range of points.
+ * @param[in] threshold rips value.
+ * @param[in] distance distance function that returns a Filtration_value from 2 given points.
+ *
+ * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a point.
+ */
+ template<typename InputPointRange, typename Point_d >
+ Rips_complex(const InputPointRange& points, Filtration_value threshold,
+ Filtration_value distance(const Point_d& p1,const Point_d& p2)) {
+ std::vector< std::pair< Vertex_handle, Vertex_handle > > edges;
+ std::vector< Filtration_value > edges_fil;
+ std::map< Vertex_handle, Filtration_value > vertices;
+
+ // Compute the proximity graph of the points.
+ // If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the
+ // distance function between points u and v is smaller than threshold.
+ // --------------------------------------------------------------------------------------------
+ // Creates the vector of edges and its filtration values (returned by distance function)
+ Vertex_handle idx_u, idx_v;
+ Filtration_value fil;
+ idx_u = 0;
+ for (auto it_u = std::begin(points); it_u != std::end(points); ++it_u) {
+ idx_v = idx_u + 1;
+ for (auto it_v = it_u + 1; it_v != std::end(points); ++it_v, ++idx_v) {
+ fil = distance(*it_u, *it_v);
+ if (fil <= threshold) {
+ edges.emplace_back(idx_u, idx_v);
+ edges_fil.push_back(fil);
+ }
+ }
+ ++idx_u;
+ }
+
+ // --------------------------------------------------------------------------------------------
+ // Creates the proximity graph from edges and sets the property with the filtration value.
+ // Number of points is labeled from 0 to idx_u-1
+ rips_skeleton_graph_ = Graph_t(edges.begin() , edges.end() , edges_fil.begin() , idx_u);
+
+ auto vertex_prop = boost::get(vertex_filtration_t(), rips_skeleton_graph_);
+
+ using vertex_iterator = typename boost::graph_traits<Graph_t>::vertex_iterator;
+ vertex_iterator vi, vi_end;
+ for (std::tie(vi, vi_end) = boost::vertices(rips_skeleton_graph_);
+ vi != vi_end; ++vi) {
+ boost::put(vertex_prop, *vi, 0.);
+ }
+
+ }
+
+ /** \brief Initializes the simplicial complex from the 1-skeleton graph and expands it until a given maximal
+ * dimension.
+ *
+ * \tparam SimplicialComplexForRips must meet `SimplicialComplexForRips` concept.
+ *
+ * @param[in] complex SimplicialComplexForRips to be created.
+ * @param[in] dim_max graph expansion for rips until this given maximal dimension.
+ *
+ * @return true if creation succeeds, false otherwise.
+ *
+ */
+ template <typename SimplicialComplexForRips>
+ bool create_complex(SimplicialComplexForRips& complex, int dim_max) {
+ if (complex.num_vertices() > 0) {
+ std::cerr << "Rips_complex create_complex - complex is not empty\n";
+ return false; // ----- >>
+ }
+
+ // insert the proximity graph in the simplicial complex
+ complex.insert_graph(rips_skeleton_graph_);
+ // expand the graph until dimension dim_max
+ complex.expansion(dim_max);
+
+ // --------------------------------------------------------------------------------------------
+ return true;
+ }
+ private:
+ Graph_t rips_skeleton_graph_;
+};
+
+} // namespace rips_complex
+
+} // namespace Gudhi
+
+#endif // RIPS_COMPLEX_H_
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 63e3f0e5..206b2fba 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -28,7 +28,7 @@
#include <gudhi/Simplex_tree/Simplex_tree_iterators.h>
#include <gudhi/Simplex_tree/indexing_tag.h>
-#include <gudhi/reader_utils.h>
+//#include <gudhi/reader_utils.h>
#include <gudhi/graph_simplicial_complex.h>
#include <gudhi/Debug_utils.h>
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index cd518581..b2726ba8 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -29,7 +29,7 @@
* by a range of coordinates. The points are assumed to have
* the same dimension. */
template< typename Point >
-double euclidean_distance(Point &p1, Point &p2) {
+double euclidean_distance(const Point &p1,const Point &p2) {
double dist = 0.;
auto it1 = p1.begin();
auto it2 = p2.begin();
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index 042ef516..773889d9 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -39,14 +39,14 @@ struct vertex_filtration_t {
typedef boost::vertex_property_tag kind;
};
-typedef int Vertex_handle;
+/*typedef int Vertex_handle;
typedef double Filtration_value;
typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
, boost::property < vertex_filtration_t, Filtration_value >
, boost::property < edge_filtration_t, Filtration_value >
> Graph_t;
typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
-
+*/
/** \brief Output the proximity graph of the points.
*
* If points contains n elements, the proximity graph is the graph
@@ -56,7 +56,7 @@ typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
* The type PointCloud furnishes .begin() and .end() methods, that return
* iterators with value_type Point.
*/
-template< typename PointCloud
+/*template< typename PointCloud
, typename Point >
Graph_t compute_proximity_graph(PointCloud &points
, Filtration_value threshold
@@ -94,6 +94,6 @@ Graph_t compute_proximity_graph(PointCloud &points
}
return skel_graph;
-}
+}*/
#endif // GRAPH_SIMPLICIAL_COMPLEX_H_
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-04 19:10:06 +0000