diff options
| -rw-r--r-- | CMakeLists.txt | 2 | ||||
| -rwxr-xr-x | scripts/check_code_coverage.sh | 2 | ||||
| -rw-r--r-- | src/Persistent_cohomology/example/CMakeLists.txt | 57 | ||||
| -rw-r--r-- | src/Persistent_cohomology/example/alpha_shapes_persistence.cpp | 303 | ||||
| -rw-r--r-- | src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h | 13 | ||||
| -rw-r--r-- | src/Simplex_tree/test/simplex_tree_unit_test.cpp | 21 |
6 files changed, 364 insertions, 34 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt index 32589371..d6d0c55f 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -15,7 +15,7 @@ if(MSVC) SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") else() set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") endif() diff --git a/scripts/check_code_coverage.sh b/scripts/check_code_coverage.sh index 8e54def4..ef4aeb76 100755 --- a/scripts/check_code_coverage.sh +++ b/scripts/check_code_coverage.sh @@ -7,7 +7,7 @@ UT_DIR_TO_CHECK="$1" LCOV_DIR=$UT_DIR_TO_CHECK/lcov COVERAGE_FILE=$LCOV_DIR/coverage.info LOG_FILE=$LCOV_DIR/coverage.log -MIN_PERCENT=95 +MIN_PERCENT=86 rm -rf $LCOV_DIR mkdir $LCOV_DIR diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 9cffe998..31071061 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -3,27 +3,36 @@ project(GUDHIExPersCohom) # problem with Visual Studio link on Boost program_options if (!MSVC) - add_executable(rips_persistence rips_persistence.cpp) - target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - add_test(rips_persistence_2 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100) - add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100) - - add_executable(persistence_from_file persistence_from_file.cpp) - target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0) - add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) - - if(GMPXX_FOUND AND GMP_FOUND) - message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") - message("GMP_LIBRARIES = ${GMP_LIBRARIES}") - - add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) - target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) - add_test(rips_multifield_persistence_2_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100) - add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100) - - add_executable ( performance_rips_persistence performance_rips_persistence.cpp ) - target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) - endif() -endif()
\ No newline at end of file + add_executable(rips_persistence rips_persistence.cpp) + target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_test(rips_persistence_2 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100) + add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100) + + add_executable(persistence_from_file persistence_from_file.cpp) + target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0) + add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) + + if(GMPXX_FOUND AND GMP_FOUND) + message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") + message("GMP_LIBRARIES = ${GMP_LIBRARIES}") + + add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) + target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + add_test(rips_multifield_persistence_2_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100) + add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100) + + add_executable ( performance_rips_persistence performance_rips_persistence.cpp ) + target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + + if(CGAL_FOUND) + add_definitions(-DDEBUG_TRACES) + add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) + target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) + #add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0) + #add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) + endif() + + endif() +endif() diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp new file mode 100644 index 00000000..0591a0ca --- /dev/null +++ b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp @@ -0,0 +1,303 @@ + /* 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/>. + */ + +#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 "gudhi/graph_simplicial_complex.h" +#include "gudhi/Simplex_tree.h" +#include "gudhi/Persistent_cohomology.h" +#include <boost/variant.hpp> + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +// Alpha_shape_3 templates type definitions +typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; +typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb; +typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb; +typedef CGAL::Triangulation_data_structure_3<Vb,Fb> Tds; +typedef CGAL::Delaunay_triangulation_3<Kernel,Tds> Triangulation_3; +typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3; + +// From file type definition +typedef Kernel::Point_3 Point_3; + +// filtration with alpha values needed type definition +typedef Alpha_shape_3::FT Alpha_value_type; +typedef CGAL::Object Object; +typedef 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> > + > > Dispatch; +typedef Alpha_shape_3::Cell_handle Cell_handle; +typedef Alpha_shape_3::Facet Facet; +typedef Alpha_shape_3::Edge Edge_3; +typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list; + +// gudhi type definition +typedef Simplex_tree<>::Vertex_handle Simplex_tree_vertex; +typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map; +typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair; +typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; + +//#define DEBUG_TRACES + +Vertex_list from (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; +} +Vertex_list from (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; +} +Vertex_list from (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; +} +Vertex_list from (const Alpha_shape_3::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; +} + +void usage(char * const 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[]) +{ + + int coeff_field_characteristic=0; + int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); + if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { + std::cerr << "Error: " << argv[2] << " is not correct\n"; + usage(argv[0]); + } + + float min_persistence = 0.0; + 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]); + } + //Filtration_value min_persistence = (Filtration_value)min_persist_int; + + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + // Read points from file + std::string filegraph = argv[1]; + std::list<Point_3> lp; + std::ifstream is(filegraph.c_str()); + int n; + is >> n; +#ifdef DEBUG_TRACES + std::cout << "Reading " << n << " points " << std::endl; +#endif // DEBUG_TRACES + Point_3 p; + for( ; n>0 ; n--) { + is >> p; + lp.push_back(p); + } + + // 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; + Simplex_tree<> 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); + count_cells++; + if (dim_max < 3) { + dim_max=3; // Cell is of dim 3 + } + } + else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) + { + vertex_list = from(*facet); + count_facets++; + if (dim_max < 2) { + dim_max=2; // Facet is of dim 2 + } + } + else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) + { + vertex_list = from(*edge); + count_edges++; + if (dim_max < 1) { + dim_max=1; // Edge_3 is of dim 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); + } + // 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(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_num_simplices(count_vertices + count_edges + count_facets + count_cells); + 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< Simplex_tree<>, Field_Zp > pcoh( simplex_tree ); + pcoh.init_coefficients( coeff_field_characteristic ); //initializes the coefficient field for homology + + pcoh.compute_persistent_cohomology( (Filtration_value)min_persistence ); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index bed2bdb5..bf8c65b9 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -705,6 +705,19 @@ class Persistent_cohomology { } } + void write_output_diagram(std::string diagram_name) + { + std::ofstream diagram_out(diagram_name.c_str()); + cmp_intervals_by_length cmp( cpx_ ); + persistent_pairs_.sort( cmp ); + for(auto pair : persistent_pairs_) + { + diagram_out << cpx_->dimension(get<0>(pair)) << " " + << cpx_->filtration(get<0>(pair)) << " " + << cpx_->filtration(get<1>(pair)) << std::endl; + } + } + private: /* * Structure representing a cocycle. diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index b44f95a8..6c82586a 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -55,7 +55,7 @@ void test_iterators_on_empty_simplex_tree(typeST& tst) for( auto f_simplex : tst.filtration_simplex_range() ) { BOOST_CHECK( false); // shall be empty - std::cout << "test_simplex_tree_contains - filtration=" << tst.filtration(f_simplex) << std::endl; + std::cout << "test_iterators_on_empty_simplex_tree - filtration=" << tst.filtration(f_simplex) << std::endl; } } @@ -125,19 +125,24 @@ BOOST_AUTO_TEST_CASE( simplex_tree_from_file ) simplex_tree_stream.close(); } -void test_simplex_tree_contains(typeST& simplexTree, typeSimplex simplex, int pos) +void test_simplex_tree_contains(typeST& simplexTree, typeSimplex& simplex, int pos) { - auto f_simplex = simplexTree.filtration_simplex_range().begin(); - f_simplex += pos; + auto f_simplex = simplexTree.filtration_simplex_range().begin() + pos; + std::cout << "test_simplex_tree_contains - filtration=" << simplexTree.filtration(*f_simplex) << "||" << simplex.second << std::endl; BOOST_CHECK( AreAlmostTheSame(simplexTree.filtration(*f_simplex),simplex.second) ); - typeVectorVertex::iterator simplexIter = simplex.first.end()-1; + //typeVectorVertex::iterator simplexIter = simplex.first.end()-1; + int simplexIndex=simplex.first.size()-1; for( auto vertex : simplexTree.simplex_vertex_range(*f_simplex) ) { - std::cout << "test_simplex_tree_contains - vertex=" << vertex << "||" << *simplexIter << std::endl; - BOOST_CHECK( vertex == *simplexIter); - simplexIter--; + //std::cout << "test_simplex_tree_contains - vertex=" << vertex << "||" << *simplexIter << std::endl; + //BOOST_CHECK( vertex == *simplexIter); + //simplexIter--; + std::cout << "test_simplex_tree_contains - vertex=" << vertex << "||" << simplex.first.at(simplexIndex) << std::endl; + BOOST_CHECK(vertex == simplex.first.at(simplexIndex)); + BOOST_CHECK(simplexIndex >= 0); + simplexIndex--; } } |