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Diffstat (limited to 'example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp')
| -rw-r--r-- | example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp | 178 |
1 files changed, 178 insertions, 0 deletions
diff --git a/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp b/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp new file mode 100644 index 00000000..ba772f04 --- /dev/null +++ b/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp @@ -0,0 +1,178 @@ +/* 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 Sophia Antipolis-Méditerranée (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> + +#include <iostream> +#include <ctime> +#include <utility> +#include <vector> + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +typedef std::vector< Vertex_handle > typeVectorVertex; +typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex; +typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool; +typedef Simplex_tree<> typeST; + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " 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 != 3) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = 0; + int returnedScanValue = sscanf(argv[1], "%d", &coeff_field_characteristic); + if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { + std::cerr << "Error: " << argv[1] << " is not correct\n"; + usage(argv[0]); + } + + Filtration_value min_persistence = 0.0; + returnedScanValue = sscanf(argv[2], "%lf", &min_persistence); + if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { + std::cerr << "Error: " << argv[2] << " is not correct\n"; + usage(argv[0]); + } + + // TEST OF INSERTION + std::cout << "********************************************************************" << std::endl; + std::cout << "TEST OF INSERTION" << std::endl; + typeST st; + + // ++ FIRST + std::cout << " - INSERT (0,1,2)" << std::endl; + typeVectorVertex SimplexVector = {0, 1, 2}; + st.insert_simplex_and_subfaces(SimplexVector, 0.3); + + // ++ SECOND + std::cout << " - INSERT 3" << std::endl; + SimplexVector = {3}; + st.insert_simplex_and_subfaces(SimplexVector, 0.1); + + // ++ THIRD + std::cout << " - INSERT (0,3)" << std::endl; + SimplexVector = {0, 3}; + st.insert_simplex_and_subfaces(SimplexVector, 0.2); + + // ++ FOURTH + std::cout << " - INSERT (0,1) (already inserted)" << std::endl; + SimplexVector = {0, 1}; + st.insert_simplex_and_subfaces(SimplexVector, 0.2); + + // ++ FIFTH + std::cout << " - INSERT (3,4,5)" << std::endl; + SimplexVector = {3, 4, 5}; + st.insert_simplex_and_subfaces(SimplexVector, 0.3); + + // ++ SIXTH + std::cout << " - INSERT (0,1,6,7)" << std::endl; + SimplexVector = {0, 1, 6, 7}; + st.insert_simplex_and_subfaces(SimplexVector, 0.4); + + // ++ SEVENTH + std::cout << " - INSERT (4,5,8,9)" << std::endl; + SimplexVector = {4, 5, 8, 9}; + st.insert_simplex_and_subfaces(SimplexVector, 0.4); + + // ++ EIGHTH + std::cout << " - INSERT (9,10,11)" << std::endl; + SimplexVector = {9, 10, 11}; + st.insert_simplex_and_subfaces(SimplexVector, 0.3); + + // ++ NINETH + std::cout << " - INSERT (2,10,12)" << std::endl; + SimplexVector = {2, 10, 12}; + st.insert_simplex_and_subfaces(SimplexVector, 0.3); + + // ++ TENTH + std::cout << " - INSERT (11,6)" << std::endl; + SimplexVector = {6, 11}; + st.insert_simplex_and_subfaces(SimplexVector, 0.2); + + // ++ ELEVENTH + std::cout << " - INSERT (13,14,15)" << std::endl; + SimplexVector = {13, 14, 15}; + st.insert_simplex_and_subfaces(SimplexVector, 0.25); + + /* Inserted simplex: */ + /* 1 6 */ + /* o---o */ + /* /X\7/ 4 2 */ + /* o---o---o---o o */ + /* 2 0 3\X/8\ 10 /X\ */ + /* o---o---o---o */ + /* 5 9\X/ 12 */ + /* o---o */ + /* 11 6 */ + /* In other words: */ + /* A facet [2,1,0] */ + /* An edge [0,3] */ + /* A facet [3,4,5] */ + /* A cell [0,1,6,7] */ + /* A cell [4,5,8,9] */ + /* A facet [9,10,11] */ + /* An edge [11,6] */ + /* An edge [10,12,2] */ + + st.set_dimension(2); + st.set_filtration(0.4); + + std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " + << std::endl; + std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" + << std::endl; + std::cout << "**************************************************************" << std::endl; + std::cout << "strict graph G { " << std::endl; + + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << " " << "[" << st.filtration(f_simplex) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << static_cast<int>(vertex) << " -- "; + } + std::cout << ";" << std::endl; + } + + std::cout << "}" << std::endl; + std::cout << "**************************************************************" << std::endl; + + // Compute the persistence diagram of the complex + persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + pcoh.output_diagram(); + return 0; +} |