summaryrefslogtreecommitdiff
path: root/src/Persistent_cohomology/example
diff options
context:
space:
mode:
authorcjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2017-05-31 16:48:08 +0000
committercjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2017-05-31 16:48:08 +0000
commit14f55cf58e9be168e6be635ddafebc6c86cc7eea (patch)
treedbe47ed41dd833626280de54ecbde703accad666 /src/Persistent_cohomology/example
parent5096889af20a04d25439ffbe5c37e663c11087bc (diff)
Convert more examples into utilities
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2494 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 54fa703f0489cba059a8df973738118f6a092f70
Diffstat (limited to 'src/Persistent_cohomology/example')
-rw-r--r--src/Persistent_cohomology/example/CMakeLists.txt35
-rw-r--r--src/Persistent_cohomology/example/alpha_complex_3d_helper.h76
-rw-r--r--src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp243
-rw-r--r--src/Persistent_cohomology/example/alpha_complex_persistence.cpp125
-rw-r--r--src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp2
-rw-r--r--src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp262
-rw-r--r--src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp144
-rw-r--r--src/Persistent_cohomology/example/rips_persistence.cpp147
-rw-r--r--src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp2
9 files changed, 2 insertions, 1034 deletions
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index a9884c49..eb31e050 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -7,12 +7,6 @@ target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
-add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
-target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-add_executable(rips_persistence rips_persistence.cpp)
-target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
target_link_libraries(rips_persistence_step_by_step ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
@@ -25,8 +19,6 @@ target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROG
if (TBB_FOUND)
target_link_libraries(plain_homology ${TBB_LIBRARIES})
target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
- target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES})
- target_link_libraries(rips_persistence ${TBB_LIBRARIES})
target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES})
target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES})
target_link_libraries(persistence_from_file ${TBB_LIBRARIES})
@@ -35,10 +27,6 @@ endif()
add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $<TARGET_FILE:plain_homology>)
add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<TARGET_FILE:persistence_from_simple_simplex_tree>
"1" "0")
-add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence>
- "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0")
-add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step>
"${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix>
@@ -50,8 +38,6 @@ add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_F
install(TARGETS plain_homology DESTINATION bin)
install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin)
-install(TARGETS rips_distance_matrix_persistence DESTINATION bin)
-install(TARGETS rips_persistence DESTINATION bin)
install(TARGETS rips_persistence_step_by_step DESTINATION bin)
install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin)
install(TARGETS persistence_from_file DESTINATION bin)
@@ -71,53 +57,32 @@ if(GMP_FOUND)
endif(GMP_FOUND)
if(CGAL_FOUND)
- add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
- target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp)
target_link_libraries(exact_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp)
target_link_libraries(weighted_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
if (TBB_FOUND)
- target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES})
target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES})
endif(TBB_FOUND)
- add_test(NAME Persistent_cohomology_example_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45")
add_test(NAME Persistent_cohomology_example_exact_alpha_complex_3d COMMAND $<TARGET_FILE:exact_alpha_complex_3d_persistence>
"${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45")
add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_alpha_complex_3d_persistence>
"${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45")
- install(TARGETS alpha_complex_3d_persistence DESTINATION bin)
install(TARGETS exact_alpha_complex_3d_persistence DESTINATION bin)
install(TARGETS weighted_alpha_complex_3d_persistence DESTINATION bin)
if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
- add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
- target_link_libraries(alpha_complex_persistence
- ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
- add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
- target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-
add_executable(custom_persistence_sort custom_persistence_sort.cpp)
target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
if (TBB_FOUND)
- target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
- target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
endif(TBB_FOUND)
- add_test(NAME Persistent_cohomology_example_alpha_complex COMMAND $<TARGET_FILE:alpha_complex_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45")
- add_test(NAME Persistent_cohomology_example_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:periodic_alpha_complex_3d_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0")
add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $<TARGET_FILE:custom_persistence_sort>)
- install(TARGETS alpha_complex_persistence DESTINATION bin)
- install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin)
install(TARGETS custom_persistence_sort DESTINATION bin)
endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
deleted file mode 100644
index 7865e4ec..00000000
--- a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
+++ /dev/null
@@ -1,76 +0,0 @@
-/* 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) 2014 INRIA Saclay (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 ALPHA_COMPLEX_3D_HELPER_H_
-#define ALPHA_COMPLEX_3D_HELPER_H_
-
-template<class Vertex_list, class Cell_handle>
-Vertex_list from_cell(const Cell_handle& ch) {
- Vertex_list the_list;
- for (auto i = 0; i < 4; i++) {
-#ifdef DEBUG_TRACES
- std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
- the_list.push_back(ch->vertex(i));
- }
- return the_list;
-}
-
-template<class Vertex_list, class Facet>
-Vertex_list from_facet(const Facet& fct) {
- Vertex_list the_list;
- for (auto i = 0; i < 4; i++) {
- if (fct.second != i) {
-#ifdef DEBUG_TRACES
- std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
- the_list.push_back(fct.first->vertex(i));
- }
- }
- return the_list;
-}
-
-template<class Vertex_list, class Edge_3>
-Vertex_list from_edge(const Edge_3& edg) {
- Vertex_list the_list;
- for (auto i = 0; i < 4; i++) {
- if ((edg.second == i) || (edg.third == i)) {
-#ifdef DEBUG_TRACES
- std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
- the_list.push_back(edg.first->vertex(i));
- }
- }
- return the_list;
-}
-
-template<class Vertex_list, class Vertex_handle>
-Vertex_list from_vertex(const Vertex_handle& vh) {
- Vertex_list the_list;
-#ifdef DEBUG_TRACES
- std::cout << "from vertex=" << vh->point() << std::endl;
-#endif // DEBUG_TRACES
- the_list.push_back(vh);
- return the_list;
-}
-
-#endif // ALPHA_COMPLEX_3D_HELPER_H_
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
deleted file mode 100644
index fd227b82..00000000
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ /dev/null
@@ -1,243 +0,0 @@
-/* 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) 2014 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/>.
- */
-
-#include <boost/variant.hpp>
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_3D_off_io.h>
-
-#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Delaunay_triangulation_3.h>
-#include <CGAL/Alpha_shape_3.h>
-#include <CGAL/iterator.h>
-
-#include <fstream>
-#include <cmath>
-#include <string>
-#include <tuple>
-#include <map>
-#include <utility>
-#include <list>
-#include <vector>
-
-#include "alpha_complex_3d_helper.h"
-
-// Alpha_shape_3 templates type definitions
-using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
-using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel>;
-using Fb = CGAL::Alpha_shape_cell_base_3<Kernel>;
-using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
-using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
-
-// From file type definition
-using Point_3 = Kernel::Point_3;
-
-// filtration with alpha values needed type definition
-using Alpha_value_type = Alpha_shape_3::FT;
-using Object = CGAL::Object;
-using Dispatch = CGAL::Dispatch_output_iterator<
- CGAL::cpp11::tuple<Object, Alpha_value_type>,
- CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
- std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
-using Cell_handle = Alpha_shape_3::Cell_handle;
-using Facet = Alpha_shape_3::Facet;
-using Edge_3 = Alpha_shape_3::Edge;
-using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
-
-// gudhi type definition
-using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = ST::Filtration_value;
-using Simplex_tree_vertex = ST::Vertex_handle;
-using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
-using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >;
-
-void usage(const std::string& progName) {
- std::cerr << "Usage: " << progName <<
- " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
- exit(-1);
-}
-
-int main(int argc, char * const argv[]) {
- // program args management
- if (argc != 4) {
- std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
- usage(argv[0]);
- }
-
- int coeff_field_characteristic = atoi(argv[2]);
-
- Filtration_value min_persistence = 0.0;
- int returnedScanValue = sscanf(argv[3], "%f", &min_persistence);
- if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
- std::cerr << "Error: " << argv[3] << " is not correct\n";
- usage(argv[0]);
- }
-
- // Read points from file
- std::string offInputFile(argv[1]);
- // Read the OFF file (input file name given as parameter) and triangulate points
- Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
- // Check the read operation was correct
- if (!off_reader.is_valid()) {
- std::cerr << "Unable to read file " << offInputFile << std::endl;
- usage(argv[0]);
- }
-
- // Retrieve the triangulation
- std::vector<Point_3> lp = off_reader.get_point_cloud();
-
- // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
- Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
-#ifdef DEBUG_TRACES
- std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
-#endif // DEBUG_TRACES
-
- // filtration with alpha values from alpha shape
- std::vector<Object> the_objects;
- std::vector<Alpha_value_type> the_alpha_values;
-
- Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
- std::back_inserter(the_alpha_values));
-
- as.filtration_with_alpha_values(disp);
-#ifdef DEBUG_TRACES
- std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
-#endif // DEBUG_TRACES
-
- Alpha_shape_3::size_type count_vertices = 0;
- Alpha_shape_3::size_type count_edges = 0;
- Alpha_shape_3::size_type count_facets = 0;
- Alpha_shape_3::size_type count_cells = 0;
-
- // Loop on objects vector
- Vertex_list vertex_list;
- ST simplex_tree;
- Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
- std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- int dim_max = 0;
- Filtration_value filtration_max = 0.0;
- for (auto object_iterator : the_objects) {
- // Retrieve Alpha shape vertex list from object
- if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
- vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
- count_cells++;
- if (dim_max < 3) {
- // Cell is of dim 3
- dim_max = 3;
- }
- } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
- vertex_list = from_facet<Vertex_list, Facet>(*facet);
- count_facets++;
- if (dim_max < 2) {
- // Facet is of dim 2
- dim_max = 2;
- }
- } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
- vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
- count_edges++;
- if (dim_max < 1) {
- // Edge_3 is of dim 1
- dim_max = 1;
- }
- } else if (const Vertex_handle * vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
- count_vertices++;
- vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
- }
- // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- Simplex_tree_vector_vertex the_simplex_tree;
- for (auto the_alpha_shape_vertex : vertex_list) {
- Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
- if (the_map_iterator == map_cgal_simplex_tree.end()) {
- // alpha shape not found
- Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
-#ifdef DEBUG_TRACES
- std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
-#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
- } else {
- // alpha shape found
- Simplex_tree_vertex vertex = the_map_iterator->second;
-#ifdef DEBUG_TRACES
- std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
-#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- }
- }
- // Construction of the simplex_tree
- Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
-#ifdef DEBUG_TRACES
- std::cout << "filtration = " << filtr << std::endl;
-#endif // DEBUG_TRACES
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
- if (the_alpha_value_iterator != the_alpha_values.end())
- ++the_alpha_value_iterator;
- else
- std::cout << "This shall not happen" << std::endl;
- }
- simplex_tree.set_filtration(filtration_max);
- simplex_tree.set_dimension(dim_max);
-
-#ifdef DEBUG_TRACES
- std::cout << "vertices \t\t" << count_vertices << std::endl;
- std::cout << "edges \t\t" << count_edges << std::endl;
- std::cout << "facets \t\t" << count_facets << std::endl;
- std::cout << "cells \t\t" << count_cells << std::endl;
-
-
- std::cout << "Information of the Simplex Tree: " << std::endl;
- std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " ";
- std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
- std::cout << " Dimension = " << simplex_tree.dimension() << " ";
- std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl;
-#endif // DEBUG_TRACES
-
-#ifdef DEBUG_TRACES
- std::cout << "Iterator on vertices: " << std::endl;
- for (auto vertex : simplex_tree.complex_vertex_range()) {
- std::cout << vertex << " ";
- }
-#endif // DEBUG_TRACES
-
- // Sort the simplices in the order of the filtration
- simplex_tree.initialize_filtration();
-
- std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
- // Compute the persistence diagram of the complex
- PCOH pcoh(simplex_tree);
- // initializes the coefficient field for homology
- pcoh.init_coefficients(coeff_field_characteristic);
-
- pcoh.compute_persistent_cohomology(min_persistence);
-
- pcoh.output_diagram();
-
- return 0;
-}
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
deleted file mode 100644
index 9e84e91f..00000000
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ /dev/null
@@ -1,125 +0,0 @@
-#include <boost/program_options.hpp>
-
-#include <CGAL/Epick_d.h>
-
-#include <gudhi/Alpha_complex.h>
-#include <gudhi/Persistent_cohomology.h>
-// to construct a simplex_tree from alpha complex
-#include <gudhi/Simplex_tree.h>
-
-#include <iostream>
-#include <string>
-#include <limits> // for numeric_limits
-
-using Simplex_tree = Gudhi::Simplex_tree<>;
-using Filtration_value = Simplex_tree::Filtration_value;
-
-void program_options(int argc, char * argv[]
- , std::string & off_file_points
- , std::string & output_file_diag
- , Filtration_value & alpha_square_max_value
- , int & coeff_field_characteristic
- , Filtration_value & min_persistence);
-
-int main(int argc, char **argv) {
- std::string off_file_points;
- std::string output_file_diag;
- Filtration_value alpha_square_max_value;
- int coeff_field_characteristic;
- Filtration_value min_persistence;
-
- program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value,
- coeff_field_characteristic, min_persistence);
-
- // ----------------------------------------------------------------------------
- // Init of an alpha complex from an OFF file
- // ----------------------------------------------------------------------------
- using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
- Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);
-
- Simplex_tree simplex;
- if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
- // ----------------------------------------------------------------------------
- // Display information about the alpha complex
- // ----------------------------------------------------------------------------
- std::cout << "Simplicial complex is of dimension " << simplex.dimension() <<
- " - " << simplex.num_simplices() << " simplices - " <<
- simplex.num_vertices() << " vertices." << std::endl;
-
- // Sort the simplices in the order of the filtration
- simplex.initialize_filtration();
-
- std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
- // Compute the persistence diagram of the complex
- Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree,
- Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex);
- // initializes the coefficient field for homology
- pcoh.init_coefficients(coeff_field_characteristic);
-
- pcoh.compute_persistent_cohomology(min_persistence);
-
- // Output the diagram in filediag
- if (output_file_diag.empty()) {
- pcoh.output_diagram();
- } else {
- std::cout << "Result in file: " << output_file_diag << std::endl;
- std::ofstream out(output_file_diag);
- pcoh.output_diagram(out);
- out.close();
- }
- }
-
- return 0;
-}
-
-void program_options(int argc, char * argv[]
- , std::string & off_file_points
- , std::string & output_file_diag
- , Filtration_value & alpha_square_max_value
- , int & coeff_field_characteristic
- , Filtration_value & min_persistence) {
- namespace po = boost::program_options;
- po::options_description hidden("Hidden options");
- hidden.add_options()
- ("input-file", po::value<std::string>(&off_file_points),
- "Name of file containing a point set. Format is one point per line: X1 ... Xd ");
-
- po::options_description visible("Allowed options", 100);
- visible.add_options()
- ("help,h", "produce help message")
- ("output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
- "Name of file in which the persistence diagram is written. Default print in std::cout")
- ("max-alpha-square-value,r",
- po::value<Filtration_value>(&alpha_square_max_value)->default_value(std::numeric_limits<Filtration_value>::infinity()),
- "Maximal alpha square value for the Alpha complex construction.")
- ("field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
- "Characteristic p of the coefficient field Z/pZ for computing homology.")
- ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
- "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
-
- po::positional_options_description pos;
- pos.add("input-file", 1);
-
- po::options_description all;
- all.add(visible).add(hidden);
-
- po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).
- options(all).positional(pos).run(), vm);
- po::notify(vm);
-
- if (vm.count("help") || !vm.count("input-file")) {
- std::cout << std::endl;
- std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
- std::cout << "of an Alpha complex defined on a set of input points.\n \n";
- std::cout << "The output diagram contains one bar per line, written with the convention: \n";
- std::cout << " p dim b d \n";
- std::cout << "where dim is the dimension of the homological feature,\n";
- std::cout << "b and d are respectively the birth and death of the feature and \n";
- std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
- std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
- std::cout << visible << std::endl;
- std::abort();
- }
-}
diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
index 8a335075..fa49dcee 100644
--- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
@@ -40,7 +40,7 @@
#include <list>
#include <vector>
-#include "alpha_complex_3d_helper.h"
+#include "../utilities/alpha_complex_3d_helper.h"
// Alpha_shape_3 templates type definitions
using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
deleted file mode 100644
index 8928cfc2..00000000
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ /dev/null
@@ -1,262 +0,0 @@
-/* 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) 2014 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/>.
- */
-
-#include <boost/variant.hpp>
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_3D_off_io.h>
-
-#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h>
-#include <CGAL/Periodic_3_Delaunay_triangulation_3.h>
-#include <CGAL/Alpha_shape_3.h>
-#include <CGAL/iterator.h>
-
-#include <fstream>
-#include <cmath>
-#include <string>
-#include <tuple>
-#include <map>
-#include <utility>
-#include <list>
-#include <vector>
-#include <cstdlib>
-
-#include "alpha_complex_3d_helper.h"
-
-// Traits
-using K = CGAL::Exact_predicates_inexact_constructions_kernel;
-using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>;
-// Vertex type
-using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
-using Vb = CGAL::Triangulation_vertex_base_3<PK, DsVb>;
-using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>;
-// Cell type
-using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>;
-using Cb = CGAL::Triangulation_cell_base_3<PK, DsCb>;
-using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>;
-using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>;
-using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3<PK, Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<P3DT3>;
-using Point_3 = PK::Point_3;
-
-// filtration with alpha values needed type definition
-using Alpha_value_type = Alpha_shape_3::FT;
-using Object = CGAL::Object;
-using Dispatch = CGAL::Dispatch_output_iterator<
- CGAL::cpp11::tuple<Object, Alpha_value_type>,
- CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
- std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
-using Cell_handle = Alpha_shape_3::Cell_handle;
-using Facet = Alpha_shape_3::Facet;
-using Edge_3 = Alpha_shape_3::Edge;
-using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
-
-// gudhi type definition
-using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = ST::Filtration_value;
-using Simplex_tree_vertex = ST::Vertex_handle;
-using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<
- ST, Gudhi::persistent_cohomology::Field_Zp >;
-
-void usage(char * const progName) {
- std::cerr << "Usage: " << progName <<
- " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
- exit(-1);
-}
-
-int main(int argc, char * const argv[]) {
- // program args management
- if (argc != 5) {
- std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
- usage(argv[0]);
- }
-
- int coeff_field_characteristic = atoi(argv[3]);
- Filtration_value min_persistence = strtof(argv[4], nullptr);
-
- // Read points from file
- std::string offInputFile(argv[1]);
- // Read the OFF file (input file name given as parameter) and triangulate points
- Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
- // Check the read operation was correct
- if (!off_reader.is_valid()) {
- std::cerr << "Unable to read file " << offInputFile << std::endl;
- usage(argv[0]);
- }
-
- // Read iso_cuboid_3 information from file
- std::ifstream iso_cuboid_str(argv[2]);
- double x_min, y_min, z_min, x_max, y_max, z_max;
- if (iso_cuboid_str.good()) {
- iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max;
- } else {
- std::cerr << "Unable to read file " << argv[2] << std::endl;
- usage(argv[0]);
- }
-
- // Retrieve the triangulation
- std::vector<Point_3> lp = off_reader.get_point_cloud();
-
- // Define the periodic cube
- P3DT3 pdt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
- // Heuristic for inserting large point sets (if pts is reasonably large)
- pdt.insert(lp.begin(), lp.end(), true);
- // As pdt won't be modified anymore switch to 1-sheeted cover if possible
- if (pdt.is_triangulation_in_1_sheet()) pdt.convert_to_1_sheeted_covering();
- std::cout << "Periodic Delaunay computed." << std::endl;
-
- // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
- // Maybe need to set it to GENERAL mode
- Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL);
-
- // filtration with alpha values from alpha shape
- std::vector<Object> the_objects;
- std::vector<Alpha_value_type> the_alpha_values;
-
- Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
- std::back_inserter(the_alpha_values));
-
- as.filtration_with_alpha_values(disp);
-#ifdef DEBUG_TRACES
- std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
-#endif // DEBUG_TRACES
-
- Alpha_shape_3::size_type count_vertices = 0;
- Alpha_shape_3::size_type count_edges = 0;
- Alpha_shape_3::size_type count_facets = 0;
- Alpha_shape_3::size_type count_cells = 0;
-
- // Loop on objects vector
- Vertex_list vertex_list;
- ST simplex_tree;
- Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
- std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- int dim_max = 0;
- Filtration_value filtration_max = 0.0;
- for (auto object_iterator : the_objects) {
- // Retrieve Alpha shape vertex list from object
- if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
- vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
- count_cells++;
- if (dim_max < 3) {
- // Cell is of dim 3
- dim_max = 3;
- }
- } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
- vertex_list = from_facet<Vertex_list, Facet>(*facet);
- count_facets++;
- if (dim_max < 2) {
- // Facet is of dim 2
- dim_max = 2;
- }
- } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
- vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
- count_edges++;
- if (dim_max < 1) {
- // Edge_3 is of dim 1
- dim_max = 1;
- }
- } else if (const Alpha_shape_3::Vertex_handle * vertex =
- CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
- count_vertices++;
- vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
- }
- // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- Simplex_tree_vector_vertex the_simplex_tree;
- for (auto the_alpha_shape_vertex : vertex_list) {
- Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
- if (the_map_iterator == map_cgal_simplex_tree.end()) {
- // alpha shape not found
- Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
-#ifdef DEBUG_TRACES
- std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
-#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
- } else {
- // alpha shape found
- Simplex_tree_vertex vertex = the_map_iterator->second;
-#ifdef DEBUG_TRACES
- std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
-#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- }
- }
- // Construction of the simplex_tree
- Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
-#ifdef DEBUG_TRACES
- std::cout << "filtration = " << filtr << std::endl;
-#endif // DEBUG_TRACES
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
- if (the_alpha_value_iterator != the_alpha_values.end())
- ++the_alpha_value_iterator;
- else
- std::cout << "This shall not happen" << std::endl;
- }
- simplex_tree.set_filtration(filtration_max);
- simplex_tree.set_dimension(dim_max);
-
-#ifdef DEBUG_TRACES
- std::cout << "vertices \t\t" << count_vertices << std::endl;
- std::cout << "edges \t\t" << count_edges << std::endl;
- std::cout << "facets \t\t" << count_facets << std::endl;
- std::cout << "cells \t\t" << count_cells << std::endl;
-
-
- std::cout << "Information of the Simplex Tree: " << std::endl;
- std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " ";
- std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
- std::cout << " Dimension = " << simplex_tree.dimension() << " ";
- std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl;
-#endif // DEBUG_TRACES
-
-#ifdef DEBUG_TRACES
- std::cout << "Iterator on vertices: " << std::endl;
- for (auto vertex : simplex_tree.complex_vertex_range()) {
- std::cout << vertex << " ";
- }
-#endif // DEBUG_TRACES
-
- // Sort the simplices in the order of the filtration
- simplex_tree.initialize_filtration();
-
- std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
- // Compute the persistence diagram of the complex
- Persistent_cohomology pcoh(simplex_tree, true);
- // initializes the coefficient field for homology
- pcoh.init_coefficients(coeff_field_characteristic);
-
- pcoh.compute_persistent_cohomology(min_persistence);
-
- pcoh.output_diagram();
-
- return 0;
-}
diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
deleted file mode 100644
index 8517e7f6..00000000
--- a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
+++ /dev/null
@@ -1,144 +0,0 @@
-/* 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): Pawel Dlotko, 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/>.
- */
-
-#include <gudhi/Rips_complex.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/reader_utils.h>
-
-#include <boost/program_options.hpp>
-
-#include <string>
-#include <vector>
-#include <limits> // infinity
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
-using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
-using Distance_matrix = std::vector<std::vector<Filtration_value>>;
-
-void program_options(int argc, char * argv[]
- , std::string & csv_matrix_file
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence);
-
-int main(int argc, char * argv[]) {
- std::string csv_matrix_file;
- std::string filediag;
- Filtration_value threshold;
- int dim_max;
- int p;
- Filtration_value min_persistence;
-
- program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
-
- Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
- Rips_complex rips_complex_from_file(distances, threshold);
-
- // Construct the Rips complex in a Simplex Tree
- Simplex_tree simplex_tree;
-
- rips_complex_from_file.create_complex(simplex_tree, dim_max);
- 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();
-
- // Compute the persistence diagram of the complex
- Persistent_cohomology 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 & csv_matrix_file
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence) {
- namespace po = boost::program_options;
- po::options_description hidden("Hidden options");
- hidden.add_options()
- ("input-file", po::value<std::string>(&csv_matrix_file),
- "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
-
- po::options_description visible("Allowed options", 100);
- visible.add_options()
- ("help,h", "produce help message")
- ("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-edge-length,r",
- po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
- "Maximal length of an edge for the Rips complex construction.")
- ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
- "Maximal dimension of the Rips complex we want to compute.")
- ("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),
- "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
-
- po::positional_options_description pos;
- pos.add("input-file", 1);
-
- po::options_description all;
- all.add(visible).add(hidden);
-
- po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).
- options(all).positional(pos).run(), vm);
- po::notify(vm);
-
- if (vm.count("help") || !vm.count("input-file")) {
- std::cout << std::endl;
- std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
- std::cout << "of a Rips complex defined on a set of distance matrix.\n \n";
- std::cout << "The output diagram contains one bar per line, written with the convention: \n";
- std::cout << " p dim b d \n";
- std::cout << "where dim is the dimension of the homological feature,\n";
- std::cout << "b and d are respectively the birth and death of the feature and \n";
- std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
- std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
- std::cout << visible << std::endl;
- std::abort();
- }
-}
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
deleted file mode 100644
index d504798b..00000000
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ /dev/null
@@ -1,147 +0,0 @@
-/* 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
- *
- * Copyright (C) 2014 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/>.
- */
-
-#include <gudhi/Rips_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_off_io.h>
-
-#include <boost/program_options.hpp>
-
-#include <string>
-#include <vector>
-#include <limits> // infinity
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
-using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
-using Point = std::vector<double>;
-using Points_off_reader = Gudhi::Points_off_reader<Point>;
-
-void program_options(int argc, char * argv[]
- , std::string & off_file_points
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence);
-
-int main(int argc, char * argv[]) {
- std::string off_file_points;
- std::string filediag;
- Filtration_value threshold;
- int dim_max;
- int p;
- Filtration_value min_persistence;
-
- program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
-
- Points_off_reader off_reader(off_file_points);
- Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
-
- // Construct the Rips complex in a Simplex Tree
- Simplex_tree simplex_tree;
-
- rips_complex_from_file.create_complex(simplex_tree, dim_max);
- 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();
-
- // Compute the persistence diagram of the complex
- Persistent_cohomology 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 & off_file_points
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence) {
- namespace po = boost::program_options;
- po::options_description hidden("Hidden options");
- hidden.add_options()
- ("input-file", po::value<std::string>(&off_file_points),
- "Name of an OFF file containing a point set.\n");
-
- po::options_description visible("Allowed options", 100);
- visible.add_options()
- ("help,h", "produce help message")
- ("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-edge-length,r",
- po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
- "Maximal length of an edge for the Rips complex construction.")
- ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
- "Maximal dimension of the Rips complex we want to compute.")
- ("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),
- "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
-
- po::positional_options_description pos;
- pos.add("input-file", 1);
-
- po::options_description all;
- all.add(visible).add(hidden);
-
- po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).
- options(all).positional(pos).run(), vm);
- po::notify(vm);
-
- if (vm.count("help") || !vm.count("input-file")) {
- std::cout << std::endl;
- std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
- std::cout << "of a Rips complex defined on a set of input points.\n \n";
- std::cout << "The output diagram contains one bar per line, written with the convention: \n";
- std::cout << " p dim b d \n";
- std::cout << "where dim is the dimension of the homological feature,\n";
- std::cout << "b and d are respectively the birth and death of the feature and \n";
- std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
- std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
- std::cout << visible << std::endl;
- std::abort();
- }
-}
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 34b90933..4a2b10f3 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -42,7 +42,7 @@
#include <vector>
#include <cstdlib>
-#include "alpha_complex_3d_helper.h"
+#include "../utilities/alpha_complex_3d_helper.h"
// Traits
using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;