From 437ccdf9616d91534af91cd8a0090b6f32d6e65b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 14 Apr 2016 12:49:09 +0000 Subject: Add of src/common/include/gudhi/Points_3D_off_io.h to read specific 3D OFF Files for CGAL Point_3 Add an example to read 3D OFF Files for CGAL Point_3 Modify alpha_complex_3d_persistence.cpp to read OFF files Add periodic_alpha_complex_3d_persistence.cpp in Persistent_cohomology examples Add info about new examples in README git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/periodic_alpha_complex_3d@1116 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6b423b598869a0f4f9c62d93c93b69efd93c0161 --- src/Persistent_cohomology/example/CMakeLists.txt | 8 +- src/Persistent_cohomology/example/README | 98 ++++++- .../example/alpha_complex_3d_persistence.cpp | 24 +- .../example/alpha_complex_persistence.cpp | 2 +- .../periodic_alpha_complex_3d_persistence.cpp | 303 +++++++++++++++++++++ 5 files changed, 414 insertions(+), 21 deletions(-) create mode 100644 src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 2f94ed15..ee6ba541 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -53,8 +53,14 @@ if(GMPXX_FOUND AND 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} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_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} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) + add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off 2 0) + if (TBB_FOUND) target_link_libraries(alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY}) endif() add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) @@ -65,7 +71,7 @@ if(GMPXX_FOUND AND GMP_FOUND) if (EIGEN3_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") include( ${EIGEN3_USE_FILE} ) - + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) target_link_libraries(alpha_complex_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README index 8c71ccf5..92b80c76 100644 --- a/src/Persistent_cohomology/example/README +++ b/src/Persistent_cohomology/example/README @@ -4,13 +4,13 @@ cd /path-to-example/ cmake . make - -Example of use : +*********************************************************************************************************************** +Example of use of RIPS: Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points sampling a Klein bottle: -./rips_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100 +./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100 output: 210 0 0 inf @@ -29,7 +29,7 @@ where with Z/3Z coefficients: -./rips_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100 +./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100 output: 3 0 0 inf @@ -37,7 +37,7 @@ output: and the computation with Z/2Z and Z/3Z coefficients simultaneously: -./rips_multifield_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100 +./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100 output: 6 0 0 inf @@ -47,10 +47,96 @@ output: and finally the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers): - ./rips_multifield_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100 + ./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100 output: 557940830126698960967415390 0 0 inf 557940830126698960967415390 1 0.0702103 inf 2 1 0.0702103 inf 2 2 0.159992 inf + +*********************************************************************************************************************** +Example of use of ALPHA: + +For a more verbose mode, please run cmake with option "DEBUG_TRACES=TRUE" and recompile the programs. + +1) 3D special case +------------------ +Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points +sampling a torus 3D: + +./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 + +output: +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 + +Here we retrieve expected Betti numbers on a tore 3D: +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 + +N.B.: alpha_complex_3d_persistence accepts only OFF files in 3D dimension. + +2) d-Dimension case +------------------- +Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points +sampling a torus 3D: + +./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off + +output: +Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 + +Here we retrieve expected Betti numbers on a tore 3D: +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 + +N.B.: alpha_complex_persistence accepts OFF files in d-Dimension. + +3) 3D periodic special case +--------------------------- +./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 2 0.0 + +output: +Periodic Delaunay computed. +Simplex_tree dim: 3 +2 0 0.0866025 inf +2 1 0.0866025 inf +2 1 0.0866025 inf +2 1 0.0866025 inf +2 2 0.0866025 inf +2 2 0.0866025 inf +2 2 0.0866025 inf + +N.B.: periodic_alpha_complex_3d_persistence accepts only OFF files in 3D dimension. In this example, the periodic cube +is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } + +*********************************************************************************************************************** +Example of use of PLAIN HOMOLOGY: + +This example computes the plain homology of the following simplicial complex without filtration values: + /* Complex to build. */ + /* 1 3 */ + /* o---o */ + /* /X\ / */ + /* o---o o */ + /* 2 0 4 */ + +./plain_homology + +output: +2 0 0 inf +2 0 0 inf +2 1 0 inf + +Here we retrieve the 2 entities {0,1,2,3} and {4} (Betti numbers[0] = 2) and the hole in {0,1,3} (Betti numbers[1] = 1) \ No newline at end of file diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index 01497c7c..48fbb91a 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -20,9 +20,9 @@ * along with this program. If not, see . */ -#include #include #include +#include #include #include @@ -139,20 +139,18 @@ int main(int argc, char * const argv[]) { } // Read points from file - std::string filegraph = argv[1]; - std::list 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); + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader 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 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 diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp index 8f9f077c..17fb84d2 100644 --- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp @@ -29,7 +29,7 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Init of an alpha complex from an OFF file // ---------------------------------------------------------------------------- - typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; + using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; Gudhi::alphacomplex::Alpha_complex alpha_complex_from_file(off_file_points, alpha_square_max_value); // ---------------------------------------------------------------------------- diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..e9425066 --- /dev/null +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_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 . + */ + +#include +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +// Traits +using K = CGAL::Exact_predicates_inexact_constructions_kernel; +using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3; +// Vertex type +using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; +using Vb = CGAL::Triangulation_vertex_base_3; +using AsVb = CGAL::Alpha_shape_vertex_base_3; +// Cell type +using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; +using Cb = CGAL::Triangulation_cell_base_3; +using AsCb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; +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, + CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > >; +using Cell_handle = Alpha_shape_3::Cell_handle; +using Facet = Alpha_shape_3::Facet; +using Edge_3 = Alpha_shape_3::Edge; +using Vertex_list = std::list; + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Alpha_shape_simplex_tree_pair = std::pair; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< + ST, Gudhi::persistent_cohomology::Field_Zp >; + +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[]) { + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + 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]); + } + + Filtration_value min_persistence = 0.0; + returnedScanValue = sscanf(argv[3], "%lf", &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 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 lp = off_reader.get_point_cloud(); + + // Define the periodic cube + P3DT3 pdt(PK::Iso_cuboid_3(0,0,0,1,1,1)); + // 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, Alpha_shape_3::GENERAL); + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(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::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(&object_iterator)) { + vertex_list = from(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from(*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(&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_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); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} -- cgit v1.2.3