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-rw-r--r--src/Witness_complex/concept/Simplicial_complex.h155
-rw-r--r--src/Witness_complex/example/CMakeLists.txt1
-rw-r--r--src/Witness_complex/example/generators.h153
-rw-r--r--src/Witness_complex/example/witness_complex_from_file.cpp77
-rw-r--r--src/Witness_complex/example/witness_complex_sphere.cpp77
-rw-r--r--src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h123
-rw-r--r--src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h103
-rw-r--r--src/Witness_complex/include/gudhi/Witness_complex.h416
-rw-r--r--src/Witness_complex/include/gudhi/Witness_complex_doc.h2
-rw-r--r--src/Witness_complex/test/CMakeLists.txt40
-rw-r--r--src/Witness_complex/test/simple_witness_complex.cpp50
-rw-r--r--src/Witness_complex/test/witness_complex_points.cpp30
12 files changed, 622 insertions, 605 deletions
diff --git a/src/Witness_complex/concept/Simplicial_complex.h b/src/Witness_complex/concept/Simplicial_complex.h
index 6b0df212..d7f3496d 100644
--- a/src/Witness_complex/concept/Simplicial_complex.h
+++ b/src/Witness_complex/concept/Simplicial_complex.h
@@ -1,83 +1,94 @@
- /* 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): Siargey Kachanovich
- *
- * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France)
- *
- * 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/>.
- */
+/* 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): Siargey Kachanovich
+ *
+ * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ * 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_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_H_
+#define CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_H_
+
+namespace Gudhi {
+
+namespace witness_complex {
/** \brief The concept Simplicial_Complex describes the requirements
- * for a type to implement a simplicial complex,
- * used for example to build a 'Witness_complex'.
- */
-struct Simplicial_complex
-{
-/** Handle to specify a simplex. */
- typedef unspecified Simplex_handle;
-/** Handle to specify a vertex. Must be a non-negative integer. */
- typedef unspecified Vertex_handle;
-
-/** Returns a Simplex_hanlde that is different from all simplex handles
- * of the simplices. */
- Simplex_handle null_simplex();
-/** \brief Returns the number of simplices in the complex.
- *
- * Does not count the empty simplex. */
- size_t num_simplices();
-
-/** \brief Iterator over the simplices of the complex,
- * in an arbitrary order.
- *
- * 'value_type' must be 'Simplex_handle'.*/
-typedef unspecified Complex_simplex_iterator;
-typedef unspecified Complex_simplex_range;
-
-/**
-* \brief Returns a range over all the simplices of a
-* complex.
-*/
-Complex_simplex_range complex_simplex_range();
-
-/** \brief Iterator over vertices of a simplex.
- *
- * 'value type' must be 'Vertex_handle'.*/
+ * for a type to implement a simplicial complex,
+ * used for example to build a 'Witness_complex'.
+ */
+struct Simplicial_complex {
+ /** Handle to specify a simplex. */
+ typedef unspecified Simplex_handle;
+ /** Handle to specify a vertex. Must be a non-negative integer. */
+ typedef unspecified Vertex_handle;
+
+ /** Returns a Simplex_hanlde that is different from all simplex handles
+ * of the simplices. */
+ Simplex_handle null_simplex();
+ /** \brief Returns the number of simplices in the complex.
+ *
+ * Does not count the empty simplex. */
+ size_t num_simplices();
+
+ /** \brief Iterator over the simplices of the complex,
+ * in an arbitrary order.
+ *
+ * 'value_type' must be 'Simplex_handle'.*/
+ typedef unspecified Complex_simplex_iterator;
+ typedef unspecified Complex_simplex_range;
+
+ /**
+ * \brief Returns a range over all the simplices of a
+ * complex.
+ */
+ Complex_simplex_range complex_simplex_range();
+
+ /** \brief Iterator over vertices of a simplex.
+ *
+ * 'value type' must be 'Vertex_handle'.*/
typedef unspecified Simplex_vertex_range;
-/** \brief Returns a range over vertices of a given
- * simplex. */
+ /** \brief Returns a range over vertices of a given
+ * simplex. */
Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex);
-
-/** \brief Return type of an insertion of a simplex
- */
+
+ /** \brief Return type of an insertion of a simplex
+ */
typedef unspecified Insertion_result_type;
-/** \brief Input range of vertices.
- * 'value_type' must be 'Vertex_handle'. */
+ /** \brief Input range of vertices.
+ * 'value_type' must be 'Vertex_handle'. */
typedef unspecified Input_vertex_range;
-
-/** \brief Inserts a simplex with vertices from a given range
- * 'vertex_range' in the simplicial complex.
- * */
- Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range);
-/** \brief Finds a simplex with vertices given by a range
- *
- * If a simplex exists, its Simplex_handle is returned.
- * Otherwise null_simplex() is returned. */
- Simplex_handle find(Input_vertex_range const & vertex_range);
+ /** \brief Inserts a simplex with vertices from a given range
+ * 'vertex_range' in the simplicial complex.
+ * */
+ Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range);
+ /** \brief Finds a simplex with vertices given by a range
+ *
+ * If a simplex exists, its Simplex_handle is returned.
+ * Otherwise null_simplex() is returned. */
+ Simplex_handle find(Input_vertex_range const & vertex_range);
};
+
+} // namespace witness_complex
+
+} // namespace Gudhi
+
+#endif // CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_H_
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index fa6dd062..b304479e 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -34,6 +34,7 @@ if(CGAL_FOUND)
add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+ add_test( witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10)
else()
message(WARNING "Eigen3 not found. Version 3.1.0 is required for witness_complex_sphere example.")
endif()
diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h
index 0d42cda2..ac445261 100644
--- a/src/Witness_complex/example/generators.h
+++ b/src/Witness_complex/example/generators.h
@@ -1,11 +1,35 @@
-#ifndef GENERATORS_H
-#define GENERATORS_H
+/* 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): Siargey Kachanovich
+ *
+ * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ * 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/>.
+ */
-#include <fstream>
+#ifndef EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+#define EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
#include <CGAL/Epick_d.h>
#include <CGAL/point_generators_d.h>
+#include <fstream>
+#include <string>
+#include <vector>
+
typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
typedef K::FT FT;
typedef K::Point_d Point_d;
@@ -18,36 +42,33 @@ typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
*
*/
inline void
-off_reader_cust ( std::string file_name , std::vector<Point_d> & points)
-{
- std::ifstream in_file (file_name.c_str(),std::ios::in);
- if(!in_file.is_open())
- {
- std::cerr << "Unable to open file " << file_name << std::endl;
- return;
- }
+off_reader_cust(std::string file_name, std::vector<Point_d> & points) {
+ std::ifstream in_file(file_name.c_str(), std::ios::in);
+ if (!in_file.is_open()) {
+ std::cerr << "Unable to open file " << file_name << std::endl;
+ return;
+ }
std::string line;
double x;
// Line OFF. No need in it
- if (!getline(in_file, line))
- {
- std::cerr << "No line OFF\n";
- return;
- }
+ if (!getline(in_file, line)) {
+ std::cerr << "No line OFF\n";
+ return;
+ }
// Line with 3 numbers. No need
- if (!getline(in_file, line))
- {
- std::cerr << "No line with 3 numbers\n";
- return;
- }
+ if (!getline(in_file, line)) {
+ std::cerr << "No line with 3 numbers\n";
+ return;
+ }
// Reading points
- while( getline ( in_file , line ) )
- {
- std::vector< double > point;
- std::istringstream iss( line );
- while(iss >> x) { point.push_back(x); }
- points.push_back(Point_d(point));
+ while (getline(in_file, line)) {
+ std::vector< double > point;
+ std::istringstream iss(line);
+ while (iss >> x) {
+ point.push_back(x);
}
+ points.push_back(Point_d(point));
+ }
in_file.close();
}
@@ -57,25 +78,24 @@ off_reader_cust ( std::string file_name , std::vector<Point_d> & points)
*
*/
inline void
-read_points_cust ( std::string file_name , Point_Vector & points)
-{
- std::ifstream in_file (file_name.c_str(),std::ios::in);
- if(!in_file.is_open())
- {
- std::cerr << "Unable to open file " << file_name << std::endl;
- return;
- }
+read_points_cust(std::string file_name, Point_Vector & points) {
+ std::ifstream in_file(file_name.c_str(), std::ios::in);
+ if (!in_file.is_open()) {
+ std::cerr << "Unable to open file " << file_name << std::endl;
+ return;
+ }
std::string line;
double x;
- while( getline ( in_file , line ) )
- {
- std::vector< double > point;
- std::istringstream iss( line );
- while(iss >> x) { point.push_back(x); }
- Point_d p(point.begin(), point.end());
- if (point.size() != 1)
- points.push_back(p);
+ while (getline(in_file, line)) {
+ std::vector< double > point;
+ std::istringstream iss(line);
+ while (iss >> x) {
+ point.push_back(x);
}
+ Point_d p(point.begin(), point.end());
+ if (point.size() != 1)
+ points.push_back(p);
+ }
in_file.close();
}
@@ -86,49 +106,42 @@ read_points_cust ( std::string file_name , Point_Vector & points)
* a flat torus, hence the opposite borders are associated.
* The points on border in this case are not placed twice.
*/
-void generate_points_grid(Point_Vector& W, int width, int D, bool torus)
-{
+void generate_points_grid(Point_Vector& W, int width, int D, bool torus) {
int nb_points = 1;
for (int i = 0; i < D; ++i)
nb_points *= width;
- for (int i = 0; i < nb_points; ++i)
- {
- std::vector<double> point;
- int cell_i = i;
- for (int l = 0; l < D; ++l)
- {
- if (torus)
- point.push_back(-1+(2.0/(width-1))*(cell_i%width));
- else
- point.push_back(-1+(2.0/width)*(cell_i%width));
- //attention: the bottom and the right are covered too!
- cell_i /= width;
- }
- W.push_back(point);
+ for (int i = 0; i < nb_points; ++i) {
+ std::vector<double> point;
+ int cell_i = i;
+ for (int l = 0; l < D; ++l) {
+ if (torus)
+ point.push_back(-1 + (2.0 / (width - 1))*(cell_i % width));
+ else
+ point.push_back(-1 + (2.0 / width)*(cell_i % width));
+ // attention: the bottom and the right are covered too!
+ cell_i /= width;
}
+ W.push_back(point);
+ }
}
/** \brief Generate nbP points uniformly in a cube of side 2
* having {+-1}^dim as its vertices and insert them in W.
*/
-void generate_points_random_box(Point_Vector& W, int nbP, int dim)
-{
+void generate_points_random_box(Point_Vector& W, int nbP, int dim) {
Random_cube_iterator rp(dim, 1.0);
- for (int i = 0; i < nbP; i++)
- {
- W.push_back(*rp++);
- }
+ for (int i = 0; i < nbP; i++) {
+ W.push_back(*rp++);
+ }
}
/** \brief Generate nbP points uniformly on a (dim-1)-sphere
* and insert them in W.
*/
-void generate_points_sphere(Point_Vector& W, int nbP, int dim)
-{
- CGAL::Random_points_on_sphere_d<Point_d> rp(dim,1);
+void generate_points_sphere(Point_Vector& W, int nbP, int dim) {
+ CGAL::Random_points_on_sphere_d<Point_d> rp(dim, 1);
for (int i = 0; i < nbP; i++)
W.push_back(*rp++);
}
-
-#endif
+#endif // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index 72caf30b..d94502b1 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -20,17 +20,19 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <iostream>
-#include <fstream>
-#include <ctime>
-
#include <sys/types.h>
#include <sys/stat.h>
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/Landmark_choice_by_random_point.h"
-#include "gudhi/reader_utils.h"
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <string>
+#include <vector>
using namespace Gudhi;
using namespace Gudhi::witness_complex;
@@ -46,24 +48,23 @@ typedef Witness_complex< Simplex_tree<> > WitnessComplex;
*
*/
inline void
-read_points_cust ( std::string file_name , std::vector< std::vector< double > > & points)
-{
- std::ifstream in_file (file_name.c_str(),std::ios::in);
- if(!in_file.is_open())
- {
- std::cerr << "Unable to open file " << file_name << std::endl;
- return;
- }
+read_points_cust(std::string file_name, std::vector< std::vector< double > > & points) {
+ std::ifstream in_file(file_name.c_str(), std::ios::in);
+ if (!in_file.is_open()) {
+ std::cerr << "Unable to open file " << file_name << std::endl;
+ return;
+ }
std::string line;
double x;
- while( getline ( in_file , line ) )
- {
- std::vector< double > point;
- std::istringstream iss( line );
- while(iss >> x) { point.push_back(x); }
- if (point.size() != 1)
- points.push_back(point);
+ while (getline(in_file, line)) {
+ std::vector< double > point;
+ std::istringstream iss(line);
+ while (iss >> x) {
+ point.push_back(x);
}
+ if (point.size() != 1)
+ points.push_back(point);
+ }
in_file.close();
}
@@ -71,25 +72,22 @@ read_points_cust ( std::string file_name , std::vector< std::vector< double > >
* Data range is a random access range of pairs (arg, value)
*/
template < typename Data_range >
-void write_data( Data_range & data, std::string filename )
-{
+void write_data(Data_range & data, std::string filename) {
std::ofstream ofs(filename, std::ofstream::out);
- for (auto entry: data)
+ for (auto entry : data)
ofs << entry.first << ", " << entry.second << "\n";
ofs.close();
}
-int main (int argc, char * const argv[])
-{
- if (argc != 3)
- {
- std::cerr << "Usage: " << argv[0]
- << " path_to_point_file nbL \n";
- return 0;
- }
+int main(int argc, char * const argv[]) {
+ if (argc != 3) {
+ std::cerr << "Usage: " << argv[0]
+ << " path_to_point_file nbL \n";
+ return 0;
+ }
- std::string file_name = argv[1];
- int nbL = atoi(argv[2]);
+ std::string file_name = argv[1];
+ int nbL = atoi(argv[2]);
clock_t start, end;
// Construct the Simplex Tree
@@ -107,13 +105,12 @@ int main (int argc, char * const argv[])
Landmark_choice_by_random_point(point_vector, nbL, knn);
end = clock();
std::cout << "Landmark choice for " << nbL << " landmarks took "
- << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-
+ << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+
// Compute witness complex
start = clock();
WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
end = clock();
std::cout << "Witness complex took "
- << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-
+ << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
}
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index 9dc458d4..36f63437 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -22,11 +22,6 @@
#define BOOST_PARAMETER_MAX_ARITY 12
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-
#include <sys/types.h>
#include <sys/stat.h>
@@ -35,6 +30,13 @@
#include <gudhi/Landmark_choice_by_random_point.h>
#include <gudhi/reader_utils.h>
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <utility>
+#include <string>
+#include <vector>
+
#include "generators.h"
using namespace Gudhi;
@@ -44,56 +46,51 @@ typedef std::vector< Vertex_handle > typeVectorVertex;
typedef Witness_complex< Simplex_tree<> > WitnessComplex;
-
/** Write a gnuplot readable file.
* Data range is a random access range of pairs (arg, value)
*/
template < typename Data_range >
-void write_data( Data_range & data, std::string filename )
-{
+void write_data(Data_range & data, std::string filename) {
std::ofstream ofs(filename, std::ofstream::out);
- for (auto entry: data)
+ for (auto entry : data)
ofs << entry.first << ", " << entry.second << "\n";
ofs.close();
}
-int main (int argc, char * const argv[])
-{
- if (argc != 2)
- {
- std::cerr << "Usage: " << argv[0]
- << " nbL \n";
- return 0;
- }
+int main(int argc, char * const argv[]) {
+ if (argc != 2) {
+ std::cerr << "Usage: " << argv[0]
+ << " nbL \n";
+ return 0;
+ }
- int nbL = atoi(argv[1]);
+ int nbL = atoi(argv[1]);
clock_t start, end;
// Construct the Simplex Tree
Simplex_tree<> simplex_tree;
- std::vector< std::pair<int, double> > l_time;
-
+ std::vector< std::pair<int, double> > l_time;
+
// Read the point file
- for (int nbP = 500; nbP < 10000; nbP += 500)
- {
- Point_Vector point_vector;
- generate_points_sphere(point_vector, nbP, 4);
- std::cout << "Successfully generated " << point_vector.size() << " points.\n";
- std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
-
- // Choose landmarks
- start = clock();
- std::vector<std::vector< int > > knn;
- Landmark_choice_by_random_point(point_vector, nbL, knn);
-
- // Compute witness complex
- WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
- end = clock();
- double time = (double)(end-start)/CLOCKS_PER_SEC;
- std::cout << "Witness complex for " << nbL << " landmarks took "
- << time << " s. \n";
- l_time.push_back(std::make_pair(nbP,time));
- }
+ for (int nbP = 500; nbP < 10000; nbP += 500) {
+ Point_Vector point_vector;
+ generate_points_sphere(point_vector, nbP, 4);
+ std::cout << "Successfully generated " << point_vector.size() << " points.\n";
+ std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
+
+ // Choose landmarks
+ start = clock();
+ std::vector<std::vector< int > > knn;
+ Landmark_choice_by_random_point(point_vector, nbL, knn);
+
+ // Compute witness complex
+ WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+ end = clock();
+ double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
+ std::cout << "Witness complex for " << nbL << " landmarks took "
+ << time << " s. \n";
+ l_time.push_back(std::make_pair(nbP, time));
+ }
write_data(l_time, "w_time.dat");
}
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
index 8dfec99c..bb7e87f5 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
@@ -23,6 +23,10 @@
#ifndef LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
#define LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
+#include <limits> // for numeric_limits<>
+#include <algorithm> // for sort
+#include <vector>
+
namespace Gudhi {
namespace witness_complex {
@@ -36,73 +40,68 @@ namespace witness_complex {
*/
class Landmark_choice_by_furthest_point {
-
-private:
+ private:
typedef std::vector<int> typeVectorVertex;
-
-public:
-
-/**
- * \brief Landmark choice strategy by iteratively adding the furthest witness from the
- * current landmark set as the new landmark.
- * \details It chooses nbL landmarks from a random access range `points` and
- * writes {witness}*{closest landmarks} matrix in `knn`.
- */
- template <typename KNearestNeighbours,
- typename Point_random_access_range>
- Landmark_choice_by_furthest_point(Point_random_access_range const &points,
- int nbL,
- KNearestNeighbours &knn)
- {
- int nb_points = points.end() - points.begin();
- assert(nb_points >= nbL);
- std::vector<std::vector<double>> wit_land_dist(nb_points, std::vector<double>()); // distance matrix witness x landmarks
- typeVectorVertex chosen_landmarks; // landmark list
-
- knn = KNearestNeighbours(nb_points, std::vector<int>());
- int current_number_of_landmarks=0; // counter for landmarks
- double curr_max_dist = 0; // used for defining the furhest point from L
- const double infty = std::numeric_limits<double>::infinity(); // infinity (see next entry)
- std::vector< double > dist_to_L(nb_points,infty); // vector of current distances to L from points
- //int dim = points.begin()->size();
-
- int rand_int = rand() % nb_points;
- int curr_max_w = rand_int; //For testing purposes a pseudo-random number is used here
-
- for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++)
- {
- //curr_max_w at this point is the next landmark
- chosen_landmarks.push_back(curr_max_w);
- unsigned i = 0;
- for (auto& p: points)
- {
- double curr_dist = euclidean_distance(p, *(points.begin() + chosen_landmarks[current_number_of_landmarks]));
- wit_land_dist[i].push_back(curr_dist);
- knn[i].push_back(current_number_of_landmarks);
- if (curr_dist < dist_to_L[i])
- dist_to_L[i] = curr_dist;
- ++i;
- }
- curr_max_dist = 0;
- for (i = 0; i < dist_to_L.size(); i++)
- if (dist_to_L[i] > curr_max_dist)
- {
- curr_max_dist = dist_to_L[i];
- curr_max_w = i;
- }
+ public:
+ /**
+ * \brief Landmark choice strategy by iteratively adding the furthest witness from the
+ * current landmark set as the new landmark.
+ * \details It chooses nbL landmarks from a random access range `points` and
+ * writes {witness}*{closest landmarks} matrix in `knn`.
+ */
+
+ template <typename KNearestNeighbours,
+ typename Point_random_access_range>
+ Landmark_choice_by_furthest_point(Point_random_access_range const &points,
+ int nbL,
+ KNearestNeighbours &knn) {
+ int nb_points = points.end() - points.begin();
+ assert(nb_points >= nbL);
+ // distance matrix witness x landmarks
+ std::vector<std::vector<double>> wit_land_dist(nb_points, std::vector<double>());
+ // landmark list
+ typeVectorVertex chosen_landmarks;
+
+ knn = KNearestNeighbours(nb_points, std::vector<int>());
+ int current_number_of_landmarks = 0; // counter for landmarks
+ double curr_max_dist = 0; // used for defining the furhest point from L
+ const double infty = std::numeric_limits<double>::infinity(); // infinity (see next entry)
+ std::vector< double > dist_to_L(nb_points, infty); // vector of current distances to L from points
+
+ // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety
+ int rand_int = rand() % nb_points;
+ int curr_max_w = rand_int; // For testing purposes a pseudo-random number is used here
+
+ for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) {
+ // curr_max_w at this point is the next landmark
+ chosen_landmarks.push_back(curr_max_w);
+ unsigned i = 0;
+ for (auto& p : points) {
+ double curr_dist = euclidean_distance(p, *(points.begin() + chosen_landmarks[current_number_of_landmarks]));
+ wit_land_dist[i].push_back(curr_dist);
+ knn[i].push_back(current_number_of_landmarks);
+ if (curr_dist < dist_to_L[i])
+ dist_to_L[i] = curr_dist;
+ ++i;
+ }
+ curr_max_dist = 0;
+ for (i = 0; i < dist_to_L.size(); i++)
+ if (dist_to_L[i] > curr_max_dist) {
+ curr_max_dist = dist_to_L[i];
+ curr_max_w = i;
}
- for (unsigned i = 0; i < points.size(); ++i)
- std::sort(knn[i].begin(),
- knn[i].end(),
- [&wit_land_dist, i](int a, int b)
- { return wit_land_dist[i][a] < wit_land_dist[i][b]; });
}
-
+ for (unsigned i = 0; i < points.size(); ++i)
+ std::sort(knn[i].begin(),
+ knn[i].end(),
+ [&wit_land_dist, i](int a, int b) {
+ return wit_land_dist[i][a] < wit_land_dist[i][b]; });
+ }
};
-}
+} // namespace witness_complex
-}
+} // namespace Gudhi
-#endif
+#endif // LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
index 3f8a8d32..215c9e65 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
@@ -23,6 +23,11 @@
#ifndef LANDMARK_CHOICE_BY_RANDOM_POINT_H_
#define LANDMARK_CHOICE_BY_RANDOM_POINT_H_
+#include <queue> // for priority_queue<>
+#include <utility> // for pair<>
+#include <vector>
+#include <set>
+
namespace Gudhi {
namespace witness_complex {
@@ -36,60 +41,56 @@ namespace witness_complex {
*/
class Landmark_choice_by_random_point {
+ public:
+ /** \brief Landmark choice strategy by taking random vertices for landmarks.
+ * \details It chooses nbL distinct landmarks from a random access range `points`
+ * and outputs a matrix {witness}*{closest landmarks} in knn.
+ */
-public:
-
- /** \brief Landmark choice strategy by taking random vertices for landmarks.
- * \details It chooses nbL distinct landmarks from a random access range `points`
- * and outputs a matrix {witness}*{closest landmarks} in knn.
- */
-
- template <typename KNearestNeighbours,
- typename Point_random_access_range>
- Landmark_choice_by_random_point(Point_random_access_range const &points,
- int nbL,
- KNearestNeighbours &knn)
- {
- int nbP = points.end() - points.begin();
- assert(nbP >= nbL);
- std::set<int> landmarks;
- int current_number_of_landmarks=0; // counter for landmarks
-
- int chosen_landmark = rand()%nbP;
- for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++)
- {
- while (landmarks.find(chosen_landmark) != landmarks.end())
- chosen_landmark = rand()% nbP;
- landmarks.insert(chosen_landmark);
- }
+ template <typename KNearestNeighbours,
+ typename Point_random_access_range>
+ Landmark_choice_by_random_point(Point_random_access_range const &points,
+ int nbL,
+ KNearestNeighbours &knn) {
+ int nbP = points.end() - points.begin();
+ assert(nbP >= nbL);
+ std::set<int> landmarks;
+ int current_number_of_landmarks = 0; // counter for landmarks
- int dim = points.begin()->size();
- typedef std::pair<double,int> dist_i;
- typedef bool (*comp)(dist_i,dist_i);
- knn = KNearestNeighbours(nbP);
- for (int points_i = 0; points_i < nbP; points_i++)
- {
- std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([&](dist_i j1, dist_i j2){return j1.first > j2.first;});
- std::set<int>::iterator landmarks_it;
- int landmarks_i = 0;
- for (landmarks_it = landmarks.begin(), landmarks_i=0; landmarks_it != landmarks.end(); landmarks_it++, landmarks_i++)
- {
- dist_i dist = std::make_pair(euclidean_distance(points[points_i],points[*landmarks_it]), landmarks_i);
- l_heap.push(dist);
- }
- for (int i = 0; i < dim+1; i++)
- {
- dist_i dist = l_heap.top();
- knn[points_i].push_back(dist.second);
- l_heap.pop();
- }
- }
+ // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety
+ int chosen_landmark = rand() % nbP;
+ for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) {
+ while (landmarks.find(chosen_landmark) != landmarks.end())
+ chosen_landmark = rand() % nbP;
+ landmarks.insert(chosen_landmark);
}
+ int dim = points.begin()->size();
+ typedef std::pair<double, int> dist_i;
+ typedef bool (*comp)(dist_i, dist_i);
+ knn = KNearestNeighbours(nbP);
+ for (int points_i = 0; points_i < nbP; points_i++) {
+ std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([&](dist_i j1, dist_i j2) {
+ return j1.first > j2.first;
+ });
+ std::set<int>::iterator landmarks_it;
+ int landmarks_i = 0;
+ for (landmarks_it = landmarks.begin(), landmarks_i = 0; landmarks_it != landmarks.end();
+ landmarks_it++, landmarks_i++) {
+ dist_i dist = std::make_pair(euclidean_distance(points[points_i], points[*landmarks_it]), landmarks_i);
+ l_heap.push(dist);
+ }
+ for (int i = 0; i < dim + 1; i++) {
+ dist_i dist = l_heap.top();
+ knn[points_i].push_back(dist.second);
+ l_heap.pop();
+ }
+ }
+ }
};
-}
-
-}
-
-#endif
+} // namespace witness_complex
+
+} // namespace Gudhi
+
+#endif // LANDMARK_CHOICE_BY_RANDOM_POINT_H_
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 819a0583..27f7a9c0 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -23,257 +23,229 @@
#ifndef WITNESS_COMPLEX_H_
#define WITNESS_COMPLEX_H_
+// Needed for the adjacency graph in bad link search
+#include <boost/graph/graph_traits.hpp>
+#include <boost/graph/adjacency_list.hpp>
+#include <boost/graph/connected_components.hpp>
+
#include <boost/container/flat_map.hpp>
#include <boost/iterator/transform_iterator.hpp>
+
+#include <gudhi/distance_functions.h>
+
#include <algorithm>
#include <utility>
-#include <gudhi/distance_functions.h>
#include <vector>
#include <list>
#include <set>
#include <queue>
#include <limits>
-#include <math.h>
#include <ctime>
#include <iostream>
-// Needed for the adjacency graph in bad link search
-#include <boost/graph/graph_traits.hpp>
-#include <boost/graph/adjacency_list.hpp>
-#include <boost/graph/connected_components.hpp>
-
namespace Gudhi {
- namespace witness_complex {
-
- /**
- \class Witness_complex
- \brief Constructs the witness complex for the given set of witnesses and landmarks.
- \ingroup witness_complex
- */
- template< class Simplicial_complex>
- class Witness_complex {
-
- private:
-
- struct Active_witness {
- int witness_id;
- int landmark_id;
-
- Active_witness(int witness_id_, int landmark_id_)
+namespace witness_complex {
+
+/**
+ \class Witness_complex
+ \brief Constructs the witness complex for the given set of witnesses and landmarks.
+ \ingroup witness_complex
+ */
+template< class Simplicial_complex>
+class Witness_complex {
+ private:
+ struct Active_witness {
+ int witness_id;
+ int landmark_id;
+
+ Active_witness(int witness_id_, int landmark_id_)
: witness_id(witness_id_),
- landmark_id(landmark_id_)
- {}
- };
+ landmark_id(landmark_id_) { }
+ };
+ private:
+ typedef typename Simplicial_complex::Simplex_handle Simplex_handle;
+ typedef typename Simplicial_complex::Vertex_handle Vertex_handle;
- private:
-
- typedef typename Simplicial_complex::Simplex_handle Simplex_handle;
- typedef typename Simplicial_complex::Vertex_handle Vertex_handle;
-
- typedef std::vector< double > Point_t;
- typedef std::vector< Point_t > Point_Vector;
+ typedef std::vector< double > Point_t;
+ typedef std::vector< Point_t > Point_Vector;
- //typedef typename Simplicial_complex::Filtration_value Filtration_value;
- typedef std::vector< Vertex_handle > typeVectorVertex;
- typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex;
- typedef std::pair< Simplex_handle, bool > typePairSimplexBool;
-
- typedef int Witness_id;
- typedef int Landmark_id;
- typedef std::list< Vertex_handle > ActiveWitnessList;
-
- private:
- int nbL; // Number of landmarks
- double density; // Desired density
- Simplicial_complex& sc; // Simplicial complex
-
- public:
+ // typedef typename Simplicial_complex::Filtration_value Filtration_value;
+ typedef std::vector< Vertex_handle > typeVectorVertex;
+ typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex;
+ typedef std::pair< Simplex_handle, bool > typePairSimplexBool;
- //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- /** @name Constructor
- */
+ typedef int Witness_id;
+ typedef int Landmark_id;
+ typedef std::list< Vertex_handle > ActiveWitnessList;
- //@{
+ private:
+ int nbL; // Number of landmarks
+ double density; // Desired density
+ Simplicial_complex& sc; // Simplicial complex
- // Witness_range<Closest_landmark_range<Vertex_handle>>
-
- /**
- * \brief Iterative construction of the witness complex.
- * \details The witness complex is written in sc_ basing on a matrix knn of
- * nearest neighbours of the form {witnesses}x{landmarks}.
- *
- * The type KNearestNeighbors can be seen as
- * Witness_range<Closest_landmark_range<Vertex_handle>>, where
- * Witness_range and Closest_landmark_range are random access ranges.
- *
- * Constructor takes into account at most (dim+1)
- * first landmarks from each landmark range to construct simplices.
- *
- * Landmarks are supposed to be in [0,nbL_-1]
- */
- template< typename KNearestNeighbors >
- Witness_complex(KNearestNeighbors const & knn,
- Simplicial_complex & sc_,
- int nbL_,
- int dim ): nbL(nbL_), sc(sc_)
- {
- //Construction of the active witness list
- int nbW = knn.size();
- typeVectorVertex vv;
- typeSimplex simplex;
- typePairSimplexBool returnValue;
- int counter = 0;
- /* The list of still useful witnesses
- * it will diminuish in the course of iterations
- */
- ActiveWitnessList active_w;// = new ActiveWitnessList();
- for (int i=0; i != nbL; ++i) {
- // initial fill of 0-dimensional simplices
- // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore
- counter++;
- vv = {i};
- returnValue = sc.insert_simplex(vv);
- /* TODO Error if not inserted : normally no need here though*/
- }
- int k=1; /* current dimension in iterative construction */
- for (int i=0; i != nbW; ++i)
- active_w.push_back(i);
- //std::cout << "Successfully added edges" << std::endl;
- while (!active_w.empty() && k < dim )
- {
- //std::cout << "Started the step k=" << k << std::endl;
- typename ActiveWitnessList::iterator it = active_w.begin();
- while (it != active_w.end())
- {
- typeVectorVertex simplex_vector;
- /* THE INSERTION: Checking if all the subfaces are in the simplex tree*/
- bool ok = all_faces_in(knn, *it, k);
- if (ok)
- {
- for (int i = 0; i != k+1; ++i)
- simplex_vector.push_back(knn[*it][i]);
- returnValue = sc.insert_simplex(simplex_vector,0.0);
- it++;
- }
- else
- active_w.erase(it++); //First increase the iterator and then erase the previous element
- }
- k++;
- }
- }
+ public:
+ /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+ /** @name Constructor
+ */
- //@}
-
- private:
-
- /** \brief Check if the facets of the k-dimensional simplex witnessed
- * by witness witness_id are already in the complex.
- * inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id
+ //@{
+
+ // Witness_range<Closest_landmark_range<Vertex_handle>>
+
+ /**
+ * \brief Iterative construction of the witness complex.
+ * \details The witness complex is written in sc_ basing on a matrix knn of
+ * nearest neighbours of the form {witnesses}x{landmarks}.
+ *
+ * The type KNearestNeighbors can be seen as
+ * Witness_range<Closest_landmark_range<Vertex_handle>>, where
+ * Witness_range and Closest_landmark_range are random access ranges.
+ *
+ * Constructor takes into account at most (dim+1)
+ * first landmarks from each landmark range to construct simplices.
+ *
+ * Landmarks are supposed to be in [0,nbL_-1]
+ */
+ template< typename KNearestNeighbors >
+ Witness_complex(KNearestNeighbors const & knn,
+ Simplicial_complex & sc_,
+ int nbL_,
+ int dim) : nbL(nbL_), sc(sc_) {
+ // Construction of the active witness list
+ int nbW = knn.size();
+ typeVectorVertex vv;
+ typeSimplex simplex;
+ typePairSimplexBool returnValue;
+ int counter = 0;
+ /* The list of still useful witnesses
+ * it will diminuish in the course of iterations
*/
- template <typename KNearestNeighbors>
- bool all_faces_in(KNearestNeighbors const &knn, int witness_id, int k)
- {
- //std::cout << "All face in with the landmark " << inserted_vertex << std::endl;
- std::vector< Vertex_handle > facet;
- //Vertex_handle curr_vh = curr_sh->first;
- // CHECK ALL THE FACETS
- for (int i = 0; i != k+1; ++i)
- {
- facet = {};
- for (int j = 0; j != k+1; ++j)
- {
- if (j != i)
- {
- facet.push_back(knn[witness_id][j]);
- }
- }//endfor
- if (sc.find(facet) == sc.null_simplex())
- return false;
- //std::cout << "++++ finished loop safely\n";
- } //endfor
- return true;
+ ActiveWitnessList active_w; // = new ActiveWitnessList();
+ for (int i = 0; i != nbL; ++i) {
+ // initial fill of 0-dimensional simplices
+ // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore
+ counter++;
+ vv = {i};
+ returnValue = sc.insert_simplex(vv);
+ // TODO(SK) Error if not inserted : normally no need here though
+ }
+ int k = 1; /* current dimension in iterative construction */
+ for (int i = 0; i != nbW; ++i)
+ active_w.push_back(i);
+ // std::cout << "Successfully added edges" << std::endl;
+ while (!active_w.empty() && k < dim) {
+ // std::cout << "Started the step k=" << k << std::endl;
+ typename ActiveWitnessList::iterator it = active_w.begin();
+ while (it != active_w.end()) {
+ typeVectorVertex simplex_vector;
+ /* THE INSERTION: Checking if all the subfaces are in the simplex tree*/
+ bool ok = all_faces_in(knn, *it, k);
+ if (ok) {
+ for (int i = 0; i != k + 1; ++i)
+ simplex_vector.push_back(knn[*it][i]);
+ returnValue = sc.insert_simplex(simplex_vector, 0.0);
+ it++;
+ } else {
+ active_w.erase(it++); // First increase the iterator and then erase the previous element
+ }
+ }
+ k++;
}
+ }
- template <typename T>
- void print_vector(const std::vector<T> v)
- {
- std::cout << "[";
- if (!v.empty())
- {
- std::cout << *(v.begin());
- for (auto it = v.begin()+1; it != v.end(); ++it)
- {
- std::cout << ",";
- std::cout << *it;
- }
+ //@}
+
+ private:
+ /** \brief Check if the facets of the k-dimensional simplex witnessed
+ * by witness witness_id are already in the complex.
+ * inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id
+ */
+ template <typename KNearestNeighbors>
+ bool all_faces_in(KNearestNeighbors const &knn, int witness_id, int k) {
+ // std::cout << "All face in with the landmark " << inserted_vertex << std::endl;
+ std::vector< Vertex_handle > facet;
+ // Vertex_handle curr_vh = curr_sh->first;
+ // CHECK ALL THE FACETS
+ for (int i = 0; i != k + 1; ++i) {
+ facet = {};
+ for (int j = 0; j != k + 1; ++j) {
+ if (j != i) {
+ facet.push_back(knn[witness_id][j]);
+ }
+ } // endfor
+ if (sc.find(facet) == sc.null_simplex())
+ return false;
+ // std::cout << "++++ finished loop safely\n";
+ } // endfor
+ return true;
+ }
+
+ template <typename T>
+ void print_vector(const std::vector<T> v) {
+ std::cout << "[";
+ if (!v.empty()) {
+ std::cout << *(v.begin());
+ for (auto it = v.begin() + 1; it != v.end(); ++it) {
+ std::cout << ",";
+ std::cout << *it;
}
- std::cout << "]";
}
-
- public:
-
- /**
- * \brief Verification if every simplex in the complex is witnessed by witnesses in knn.
- * \param print_output =true will print the witnesses for each simplex
- * \remark Added for debugging purposes.
- */
- template< class KNearestNeighbors >
- bool is_witness_complex(KNearestNeighbors const & knn, bool print_output)
- {
- //bool final_result = true;
- for (Simplex_handle sh: sc.complex_simplex_range())
- {
- bool is_witnessed = false;
- typeVectorVertex simplex;
- int nbV = 0; //number of verticed in the simplex
- for (int v: sc.simplex_vertex_range(sh))
- simplex.push_back(v);
- nbV = simplex.size();
- for (typeVectorVertex w: knn)
- {
- bool has_vertices = true;
- for (int v: simplex)
- if (std::find(w.begin(), w.begin()+nbV, v) == w.begin()+nbV)
- {
- has_vertices = false;
- //break;
- }
- if (has_vertices)
- {
- is_witnessed = true;
- if (print_output)
- {
- std::cout << "The simplex ";
- print_vector(simplex);
- std::cout << " is witnessed by the witness ";
- print_vector(w);
- std::cout << std::endl;
- }
- break;
- }
- }
- if (!is_witnessed)
- {
- if (print_output)
- {
- std::cout << "The following simplex is not witnessed ";
- print_vector(simplex);
- std::cout << std::endl;
- }
- assert(is_witnessed);
- return false;
- }
+ std::cout << "]";
+ }
+
+ public:
+ /**
+ * \brief Verification if every simplex in the complex is witnessed by witnesses in knn.
+ * \param print_output =true will print the witnesses for each simplex
+ * \remark Added for debugging purposes.
+ */
+ template< class KNearestNeighbors >
+ bool is_witness_complex(KNearestNeighbors const & knn, bool print_output) {
+ // bool final_result = true;
+ for (Simplex_handle sh : sc.complex_simplex_range()) {
+ bool is_witnessed = false;
+ typeVectorVertex simplex;
+ int nbV = 0; // number of verticed in the simplex
+ for (int v : sc.simplex_vertex_range(sh))
+ simplex.push_back(v);
+ nbV = simplex.size();
+ for (typeVectorVertex w : knn) {
+ bool has_vertices = true;
+ for (int v : simplex)
+ if (std::find(w.begin(), w.begin() + nbV, v) == w.begin() + nbV) {
+ has_vertices = false;
+ // break;
+ }
+ if (has_vertices) {
+ is_witnessed = true;
+ if (print_output) {
+ std::cout << "The simplex ";
+ print_vector(simplex);
+ std::cout << " is witnessed by the witness ";
+ print_vector(w);
+ std::cout << std::endl;
+ }
+ break;
+ }
+ }
+ if (!is_witnessed) {
+ if (print_output) {
+ std::cout << "The following simplex is not witnessed ";
+ print_vector(simplex);
+ std::cout << std::endl;
}
- return true;
+ assert(is_witnessed);
+ return false;
+ }
}
+ return true;
+ }
+};
-
- }; //class Witness_complex
+} // namespace witness_complex
- } //namespace witness_complex
-
-} // namespace Guhdi
+} // namespace Gudhi
-#endif
+#endif // WITNESS_COMPLEX_H_
diff --git a/src/Witness_complex/include/gudhi/Witness_complex_doc.h b/src/Witness_complex/include/gudhi/Witness_complex_doc.h
index dbe9e7ce..e9f78170 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex_doc.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex_doc.h
@@ -35,4 +35,4 @@
*/
-#endif
+#endif // WITNESS_COMPLEX_DOC_H_
diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index a13fd94a..9422c152 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -1,16 +1,34 @@
cmake_minimum_required(VERSION 2.6)
-project(GUDHITestWitnessComplex)
+project(GUDHIWitnessComplexUT)
-#if(NOT MSVC)
-# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-# set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage")
-# set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage")
-#endif()
+if (GCOVR_PATH)
+ # for gcovr to make coverage reports - Corbera Jenkins plugin
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")
+ set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+ # for gprof to make coverage reports - Jenkins
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
+ set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
+endif()
-add_executable ( simple_witness_complex simple_witness_complex.cpp )
-add_test(test ${CMAKE_CURRENT_BINARY_DIR}/simple_witness_complex)
+add_executable ( simple_witness_complexUT simple_witness_complex.cpp )
+target_link_libraries(simple_witness_complexUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-add_executable ( witness_complex_points witness_complex_points.cpp )
-add_test(test ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_points)
+# Unitary tests definition and xml result file generation
+add_test(NAME simple_witness_complexUT
+ COMMAND ${CMAKE_CURRENT_BINARY_DIR}/simple_witness_complexUT
+ # XML format for Jenkins xUnit plugin
+ --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
+
+add_executable ( witness_complex_pointsUT witness_complex_points.cpp )
+target_link_libraries(witness_complex_pointsUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+
+# Unitary tests definition and xml result file generation
+add_test(NAME witness_complex_pointsUT
+ COMMAND ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_pointsUT
+ # XML format for Jenkins xUnit plugin
+ --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/witness_complex_pointsUT.xml --log_level=test_suite --report_level=no)
-#cpplint_add_tests("${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi")
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index 7735ca6f..7d44b90c 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -20,34 +20,40 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <iostream>
-#include <ctime>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "simple_witness_complex"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
#include <gudhi/Simplex_tree.h>
#include <gudhi/Witness_complex.h>
-using namespace Gudhi;
-using namespace Gudhi::witness_complex;
+#include <iostream>
+#include <ctime>
+#include <vector>
+typedef Gudhi::Simplex_tree<> Simplex_tree;
typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef Witness_complex<Simplex_tree<>> WitnessComplex;
+typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex;
-int main (int argc, char * const argv[])
-{
- Simplex_tree<> complex;
+BOOST_AUTO_TEST_CASE(simple_witness_complex) {
+ Simplex_tree complex;
std::vector< typeVectorVertex > knn;
- typeVectorVertex witness0 = {1,0,5,2,6,3,4}; knn.push_back(witness0 );
- typeVectorVertex witness1 = {2,6,4,5,0,1,3}; knn.push_back(witness1 );
- typeVectorVertex witness2 = {3,4,2,1,5,6,0}; knn.push_back(witness2 );
- typeVectorVertex witness3 = {4,2,1,3,5,6,0}; knn.push_back(witness3 );
- typeVectorVertex witness4 = {5,1,6,0,2,3,4}; knn.push_back(witness4 );
- typeVectorVertex witness5 = {6,0,5,2,1,3,4}; knn.push_back(witness5 );
- typeVectorVertex witness6 = {0,5,6,1,2,3,4}; knn.push_back(witness6 );
- typeVectorVertex witness7 = {2,6,4,5,3,1,0}; knn.push_back(witness7 );
- typeVectorVertex witness8 = {1,2,5,4,3,6,0}; knn.push_back(witness8 );
- typeVectorVertex witness9 = {3,4,0,6,5,1,2}; knn.push_back(witness9 );
- typeVectorVertex witness10 = {5,0,1,3,6,2,4}; knn.push_back(witness10);
- typeVectorVertex witness11 = {5,6,1,0,2,3,4}; knn.push_back(witness11);
- typeVectorVertex witness12 = {1,6,0,5,2,3,4}; knn.push_back(witness12);
+
+ knn.push_back({1, 0, 5, 2, 6, 3, 4});
+ knn.push_back({2, 6, 4, 5, 0, 1, 3});
+ knn.push_back({3, 4, 2, 1, 5, 6, 0});
+ knn.push_back({4, 2, 1, 3, 5, 6, 0});
+ knn.push_back({5, 1, 6, 0, 2, 3, 4});
+ knn.push_back({6, 0, 5, 2, 1, 3, 4});
+ knn.push_back({0, 5, 6, 1, 2, 3, 4});
+ knn.push_back({2, 6, 4, 5, 3, 1, 0});
+ knn.push_back({1, 2, 5, 4, 3, 6, 0});
+ knn.push_back({3, 4, 0, 6, 5, 1, 2});
+ knn.push_back({5, 0, 1, 3, 6, 2, 4});
+ knn.push_back({5, 6, 1, 0, 2, 3, 4});
+ knn.push_back({1, 6, 0, 5, 2, 3, 4});
WitnessComplex witnessComplex(knn, complex, 7, 7);
- assert(witnessComplex.is_witness_complex(knn, false));
+
+ BOOST_CHECK(witnessComplex.is_witness_complex(knn, false));
}
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index 3850bd82..78f01e08 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -20,36 +20,38 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#include <iostream>
-#include <ctime>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "witness_complex_points"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
#include <gudhi/Simplex_tree.h>
#include <gudhi/Witness_complex.h>
#include <gudhi/Landmark_choice_by_random_point.h>
#include <gudhi/Landmark_choice_by_furthest_point.h>
+#include <iostream>
+#include <vector>
-using namespace Gudhi;
-using namespace Gudhi::witness_complex;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef Witness_complex<Simplex_tree<>> WitnessComplex;
typedef std::vector<double> Point;
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
+typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef Gudhi::Simplex_tree<> Simplex_tree;
+typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex;
+typedef Gudhi::witness_complex::Landmark_choice_by_random_point Landmark_choice_by_random_point;
+typedef Gudhi::witness_complex::Landmark_choice_by_furthest_point Landmark_choice_by_furthest_point;
-int main (int argc, char * const argv[])
-{
+BOOST_AUTO_TEST_CASE(witness_complex_points) {
std::vector< typeVectorVertex > knn;
std::vector< Point > points;
// Add grid points as witnesses
for (double i = 0; i < 10; i += 1.0)
for (double j = 0; j < 10; j += 1.0)
for (double k = 0; k < 10; k += 1.0)
- points.push_back(Point({i,j,k}));
+ points.push_back(Point({i, j, k}));
bool b_print_output = false;
// First test: random choice
- Simplex_tree<> complex1;
+ Simplex_tree complex1;
Landmark_choice_by_random_point lcrp(points, 100, knn);
assert(!knn.empty());
WitnessComplex witnessComplex1(knn, complex1, 100, 3);
@@ -57,7 +59,7 @@ int main (int argc, char * const argv[])
// Second test: furthest choice
knn.clear();
- Simplex_tree<> complex2;
+ Simplex_tree complex2;
Landmark_choice_by_furthest_point lcfp(points, 100, knn);
WitnessComplex witnessComplex2(knn, complex2, 100, 3);
assert(witnessComplex2.is_witness_complex(knn, b_print_output));
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-28 11:00:55 +0000