summaryrefslogtreecommitdiff
path: root/src/Witness_complex
diff options
context:
space:
mode:
Diffstat (limited to 'src/Witness_complex')
-rw-r--r--src/Witness_complex/doc/Witness_complex_doc.h13
-rw-r--r--src/Witness_complex/example/CMakeLists.txt32
-rw-r--r--src/Witness_complex/example/example_strong_witness_complex_off.cpp24
-rw-r--r--src/Witness_complex/example/example_witness_complex_off.cpp6
-rw-r--r--src/Witness_complex/example/example_witness_complex_sphere.cpp26
-rw-r--r--src/Witness_complex/include/gudhi/Strong_witness_complex.h6
-rw-r--r--src/Witness_complex/utilities/CMakeLists.txt28
-rw-r--r--src/Witness_complex/utilities/strong_witness_persistence.cpp (renamed from src/Witness_complex/example/example_strong_witness_persistence.cpp)71
-rw-r--r--src/Witness_complex/utilities/weak_witness_persistence.cpp (renamed from src/Witness_complex/example/example_witness_complex_persistence.cpp)71
-rw-r--r--src/Witness_complex/utilities/witnesscomplex.md66
10 files changed, 200 insertions, 143 deletions
diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h
index 171a185f..62203054 100644
--- a/src/Witness_complex/doc/Witness_complex_doc.h
+++ b/src/Witness_complex/doc/Witness_complex_doc.h
@@ -90,8 +90,9 @@ int main(int argc, char * const argv[]) {
Gudhi::Points_off_reader<Point_d> off_reader(file_name);
point_vector = Point_vector(off_reader.get_point_cloud());
- // Choose landmarks
- Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+ // Choose landmarks (one can choose either of the two methods below)
+ // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+ Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
// Compute witness complex
Witness_complex witness_complex(landmarks,
@@ -107,10 +108,14 @@ int main(int argc, char * const argv[]) {
Here is an example of constructing a strong witness complex filtration and computing persistence on it:
- \include Witness_complex/example_strong_witness_persistence.cpp
+ \include Witness_complex/strong_witness_persistence.cpp
- \copyright GNU General Public License v3.
+ \section witnessexample3 Example3: Computing relaxed witness complex persistence from a distance matrix
+ In this example we compute the relaxed witness complex persistence from a given matrix of closest landmarks to each witness.
+ Each landmark is given as the couple (index, distance).
+
+ \include Witness_complex/example_nearest_landmark_table.cpp
*/
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index cbc53902..a8231392 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -13,39 +13,23 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin)
# CGAL and Eigen3 are required for Euclidean version of Witness
if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
- add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
-
- add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp )
- target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
- add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
- target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
- if (TBB_FOUND)
- target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES})
- target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
- endif()
+
+ add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
+ target_link_libraries(Witness_complex_example_strong_off)
add_test(NAME Witness_complex_example_off_test_torus
COMMAND $<TARGET_FILE:Witness_complex_example_off>
"${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
+ add_test(NAME Witness_complex_example_test_sphere_10
+ COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10")
add_test(NAME Witness_complex_example_strong_off_test_torus
COMMAND $<TARGET_FILE:Witness_complex_example_strong_off>
"${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
- add_test(NAME Witness_complex_example_test_sphere_10
- COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10")
- add_test(NAME Witness_complex_example_test_torus_persistence
- COMMAND $<TARGET_FILE:Witness_complex_example_witness_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
- add_test(NAME Witness_complex_example_strong_test_torus_persistence
- COMMAND $<TARGET_FILE:Witness_complex_example_strong_witness_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
-
+
install(TARGETS Witness_complex_example_off DESTINATION bin)
- install(TARGETS Witness_complex_example_strong_off DESTINATION bin)
install(TARGETS Witness_complex_example_sphere DESTINATION bin)
- install(TARGETS Witness_complex_example_witness_persistence DESTINATION bin)
- install(TARGETS Witness_complex_example_strong_witness_persistence DESTINATION bin)
+ install(TARGETS Witness_complex_example_strong_off DESTINATION bin)
+
endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
index 0ee9ee90..346bef6d 100644
--- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
@@ -23,6 +23,7 @@
#include <gudhi/Simplex_tree.h>
#include <gudhi/Euclidean_strong_witness_complex.h>
#include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
#include <gudhi/Points_off_io.h>
#include <CGAL/Epick_d.h>
@@ -38,10 +39,9 @@ using Point_d = typename K::Point_d;
using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>;
using Point_vector = std::vector<Point_d>;
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
if (argc != 5) {
- std::cerr << "Usage: " << argv[0]
- << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
+ std::cerr << "Usage: " << argv[0] << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
return 0;
}
@@ -55,25 +55,25 @@ int main(int argc, char * const argv[]) {
Point_vector point_vector, landmarks;
Gudhi::Points_off_reader<Point_d> off_reader(file_name);
if (!off_reader.is_valid()) {
- std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n";
- exit(-1); // ----- >>
- }
+ std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n";
+ exit(-1); // ----- >>
+ }
point_vector = Point_vector(off_reader.get_point_cloud());
std::cout << "Successfully read " << point_vector.size() << " points.\n";
std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
- // Choose landmarks
- Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+ // Choose landmarks (decomment one of the following two lines)
+ // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+ Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point,
+ std::back_inserter(landmarks));
// Compute witness complex
start = clock();
- Witness_complex witness_complex(landmarks,
- point_vector);
+ Witness_complex witness_complex(landmarks, point_vector);
witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
end = clock();
- std::cout << "Strong witness complex took "
- << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+ std::cout << "Strong witness complex took " << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
}
diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp
index b36dac0d..be11c955 100644
--- a/src/Witness_complex/example/example_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_witness_complex_off.cpp
@@ -4,6 +4,7 @@
#include <gudhi/Simplex_tree.h>
#include <gudhi/Euclidean_witness_complex.h>
#include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
#include <gudhi/Points_off_io.h>
#include <CGAL/Epick_d.h>
@@ -44,8 +45,9 @@ int main(int argc, char * const argv[]) {
std::cout << "Successfully read " << point_vector.size() << " points.\n";
std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
- // Choose landmarks
- Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+ // Choose landmarks (decomment one of the following two lines)
+ // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+ Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
// Compute witness complex
start = clock();
diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp
index 124fd99b..a6e9b11a 100644
--- a/src/Witness_complex/example/example_witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp
@@ -25,6 +25,7 @@
#include <gudhi/Simplex_tree.h>
#include <gudhi/Euclidean_witness_complex.h>
#include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
#include <gudhi/reader_utils.h>
#include <CGAL/Epick_d.h>
@@ -41,27 +42,25 @@
/** 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) {
+template <typename Data_range>
+void write_data(Data_range& data, std::string filename) {
std::ofstream ofs(filename, std::ofstream::out);
- for (auto entry : data)
- ofs << entry.first << ", " << entry.second << "\n";
+ for (auto entry : data) ofs << entry.first << ", " << entry.second << "\n";
ofs.close();
}
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<Kernel>;
if (argc != 2) {
- std::cerr << "Usage: " << argv[0]
- << " number_of_landmarks \n";
+ std::cerr << "Usage: " << argv[0] << " number_of_landmarks \n";
return 0;
}
int number_of_landmarks = atoi(argv[1]);
- std::vector< std::pair<int, double> > l_time;
+ std::vector<std::pair<int, double> > l_time;
// Generate points
for (int nbP = 500; nbP < 10000; nbP += 500) {
@@ -75,16 +74,17 @@ int main(int argc, char * const argv[]) {
// Choose landmarks
start = clock();
- Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks));
+ // Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks));
+ Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, number_of_landmarks,
+ Gudhi::subsampling::random_starting_point,
+ std::back_inserter(landmarks));
// Compute witness complex
- Witness_complex witness_complex(landmarks,
- point_vector);
+ Witness_complex witness_complex(landmarks, point_vector);
witness_complex.create_complex(simplex_tree, 0);
end = clock();
double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
- std::cout << "Witness complex for " << number_of_landmarks << " landmarks took "
- << time << " s. \n";
+ std::cout << "Witness complex for " << number_of_landmarks << " landmarks took " << time << " s. \n";
std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
l_time.push_back(std::make_pair(nbP, time));
}
diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
index c18335d3..b3d00b11 100644
--- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
@@ -34,7 +34,8 @@ namespace Gudhi {
namespace witness_complex {
-/* \private
+ /**
+ * \private
* \class Strong_witness_complex
* \brief Constructs strong witness complex for a given table of nearest landmarks with respect to witnesses.
* \ingroup witness_complex
@@ -130,6 +131,8 @@ class Strong_witness_complex {
return true;
}
+ //@}
+
private:
/* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness.
* Iterator is needed to know until how far we can take landmarks to form simplexes.
@@ -170,7 +173,6 @@ class Strong_witness_complex {
simplex.pop_back();
}
}
- //@}
};
} // namespace witness_complex
diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt
new file mode 100644
index 00000000..125a41ff
--- /dev/null
+++ b/src/Witness_complex/utilities/CMakeLists.txt
@@ -0,0 +1,28 @@
+cmake_minimum_required(VERSION 2.6)
+project(Witness_complex_utilities)
+
+# CGAL and Eigen3 are required for Euclidean version of Witness
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+
+ add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp )
+ target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+ add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp )
+ target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+ if (TBB_FOUND)
+ target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES})
+ target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES})
+ endif()
+
+ add_test(NAME Witness_complex_strong_test_torus_persistence
+ COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
+ add_test(NAME Witness_complex_weak_test_torus_persistence
+ COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
+
+ install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin)
+ install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin)
+
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp
index f786fe7b..2fba631b 100644
--- a/src/Witness_complex/example/example_strong_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp
@@ -25,6 +25,7 @@
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Points_off_io.h>
#include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
#include <boost/program_options.hpp>
@@ -46,16 +47,10 @@ using Filtration_value = SimplexTree::Filtration_value;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>;
-void program_options(int argc, char * argv[]
- , int & nbL
- , std::string & file_name
- , std::string & filediag
- , Filtration_value & max_squared_alpha
- , int & p
- , int & dim_max
- , Filtration_value & min_persistence);
+void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
+ Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence);
-int main(int argc, char * argv[]) {
+int main(int argc, char* argv[]) {
std::string file_name;
std::string filediag;
Filtration_value max_squared_alpha;
@@ -69,19 +64,20 @@ int main(int argc, char * argv[]) {
Point_vector witnesses, landmarks;
Gudhi::Points_off_reader<Point_d> off_reader(file_name);
if (!off_reader.is_valid()) {
- std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
- exit(-1); // ----- >>
+ std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+ exit(-1); // ----- >>
}
witnesses = Point_vector(off_reader.get_point_cloud());
std::cout << "Successfully read " << witnesses.size() << " points.\n";
std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
- // Choose landmarks from witnesses
- Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+ // Choose landmarks (decomment one of the following two lines)
+ // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+ Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point,
+ std::back_inserter(landmarks));
// Compute witness complex
- Strong_witness_complex strong_witness_complex(landmarks,
- witnesses);
+ Strong_witness_complex strong_witness_complex(landmarks, witnesses);
strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
@@ -110,37 +106,28 @@ int main(int argc, char * argv[]) {
return 0;
}
-void program_options(int argc, char * argv[]
- , int & nbL
- , std::string & file_name
- , std::string & filediag
- , Filtration_value & max_squared_alpha
- , int & p
- , int & dim_max
- , Filtration_value & min_persistence) {
+void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
+ Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence) {
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
- hidden.add_options()
- ("input-file", po::value<std::string>(&file_name),
- "Name of file containing a point set in off format.");
+ hidden.add_options()("input-file", po::value<std::string>(&file_name),
+ "Name of file containing a point set in off format.");
po::options_description visible("Allowed options", 100);
Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity();
- visible.add_options()
- ("help,h", "produce help message")
- ("landmarks,l", po::value<int>(&nbL),
- "Number of landmarks to choose from the point cloud.")
- ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
- "Name of file in which the persistence diagram is written. Default print in std::cout")
- ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
- "Maximal squared relaxation parameter.")
- ("field-charac,p", po::value<int>(&p)->default_value(11),
- "Characteristic p of the coefficient field Z/pZ for computing homology.")
- ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
- "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals")
- ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
- "Maximal dimension of the strong witness complex we want to compute.");
+ visible.add_options()("help,h", "produce help message")("landmarks,l", po::value<int>(&nbL),
+ "Number of landmarks to choose from the point cloud.")(
+ "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+ "Name of file in which the persistence diagram is written. Default print in std::cout")(
+ "max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
+ "Maximal squared relaxation parameter.")(
+ "field-charac,p", po::value<int>(&p)->default_value(11),
+ "Characteristic p of the coefficient field Z/pZ for computing homology.")(
+ "min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
+ "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
+ "intervals")("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
+ "Maximal dimension of the strong witness complex we want to compute.");
po::positional_options_description pos;
pos.add("input-file", 1);
@@ -149,8 +136,7 @@ void program_options(int argc, char * argv[]
all.add(visible).add(hidden);
po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).
- options(all).positional(pos).run(), vm);
+ po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
po::notify(vm);
if (vm.count("help") || !vm.count("input-file")) {
@@ -168,4 +154,3 @@ void program_options(int argc, char * argv[]
std::abort();
}
}
-
diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp
index a1146922..23fa93aa 100644
--- a/src/Witness_complex/example/example_witness_complex_persistence.cpp
+++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp
@@ -25,6 +25,7 @@
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Points_off_io.h>
#include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
#include <boost/program_options.hpp>
@@ -46,16 +47,10 @@ using Filtration_value = SimplexTree::Filtration_value;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>;
-void program_options(int argc, char * argv[]
- , int & nbL
- , std::string & file_name
- , std::string & filediag
- , Filtration_value & max_squared_alpha
- , int & p
- , int & dim_max
- , Filtration_value & min_persistence);
+void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
+ Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence);
-int main(int argc, char * argv[]) {
+int main(int argc, char* argv[]) {
std::string file_name;
std::string filediag;
Filtration_value max_squared_alpha;
@@ -69,19 +64,20 @@ int main(int argc, char * argv[]) {
Point_vector witnesses, landmarks;
Gudhi::Points_off_reader<Point_d> off_reader(file_name);
if (!off_reader.is_valid()) {
- std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
- exit(-1); // ----- >>
+ std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+ exit(-1); // ----- >>
}
witnesses = Point_vector(off_reader.get_point_cloud());
std::cout << "Successfully read " << witnesses.size() << " points.\n";
std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
- // Choose landmarks from witnesses
- Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+ // Choose landmarks (decomment one of the following two lines)
+ // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+ Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point,
+ std::back_inserter(landmarks));
// Compute witness complex
- Witness_complex witness_complex(landmarks,
- witnesses);
+ Witness_complex witness_complex(landmarks, witnesses);
witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
@@ -110,38 +106,28 @@ int main(int argc, char * argv[]) {
return 0;
}
-
-void program_options(int argc, char * argv[]
- , int & nbL
- , std::string & file_name
- , std::string & filediag
- , Filtration_value & max_squared_alpha
- , int & p
- , int & dim_max
- , Filtration_value & min_persistence) {
+void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
+ Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence) {
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
- hidden.add_options()
- ("input-file", po::value<std::string>(&file_name),
- "Name of file containing a point set in off format.");
+ hidden.add_options()("input-file", po::value<std::string>(&file_name),
+ "Name of file containing a point set in off format.");
Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity();
po::options_description visible("Allowed options", 100);
- visible.add_options()
- ("help,h", "produce help message")
- ("landmarks,l", po::value<int>(&nbL),
- "Number of landmarks to choose from the point cloud.")
- ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
- "Name of file in which the persistence diagram is written. Default print in std::cout")
- ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
- "Maximal squared relaxation parameter.")
- ("field-charac,p", po::value<int>(&p)->default_value(11),
- "Characteristic p of the coefficient field Z/pZ for computing homology.")
- ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
- "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals")
- ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
- "Maximal dimension of the weak witness complex we want to compute.");
+ visible.add_options()("help,h", "produce help message")("landmarks,l", po::value<int>(&nbL),
+ "Number of landmarks to choose from the point cloud.")(
+ "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+ "Name of file in which the persistence diagram is written. Default print in std::cout")(
+ "max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
+ "Maximal squared relaxation parameter.")(
+ "field-charac,p", po::value<int>(&p)->default_value(11),
+ "Characteristic p of the coefficient field Z/pZ for computing homology.")(
+ "min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
+ "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
+ "intervals")("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
+ "Maximal dimension of the weak witness complex we want to compute.");
po::positional_options_description pos;
pos.add("input-file", 1);
@@ -150,8 +136,7 @@ void program_options(int argc, char * argv[]
all.add(visible).add(hidden);
po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).
- options(all).positional(pos).run(), vm);
+ po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
po::notify(vm);
if (vm.count("help") || !vm.count("input-file")) {
diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md
new file mode 100644
index 00000000..2341759b
--- /dev/null
+++ b/src/Witness_complex/utilities/witnesscomplex.md
@@ -0,0 +1,66 @@
+
+
+# Witness complex #
+
+
+For more details about the witness complex, please read the [user manual of the package](/doc/latest/group__witness__complex.html).
+
+## weak_witness_persistence ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points.
+The output diagram contains one bar per line, written with the convention:
+
+`p dim birth death`
+
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,
+and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+**Usage**
+
+`weak_witness_persistence [options] <OFF input file>`
+
+**Allowed options**
+
+* `-h [ --help ]` Produce help message
+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.
+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
+
+**Example**
+
+`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`
+
+N.B.: output is random as the 20 landmarks are chosen randomly.
+
+
+## strong_witness_persistence ##
+
+This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points.
+The output diagram contains one bar per line, written with the convention:
+
+`p dim birth death`
+
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,
+and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+**Usage**
+
+`strong_witness_persistence [options] <OFF input file>`
+
+**Allowed options**
+
+* `-h [ --help ]` Produce help message
+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.
+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
+
+**Example**
+
+`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`
+
+N.B.: output is random as the 20 landmarks are chosen randomly.
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-29 12:05:54 +0000