diff options
Diffstat (limited to 'src/Persistent_cohomology')
8 files changed, 2 insertions, 31 deletions
diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 46b784d8..b4f9fd2c 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -21,7 +21,7 @@ namespace persistent_cohomology { \author Clément Maria Computation of persistent cohomology using the algorithm of - \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:journals/corr/abs-1208-5018 + \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:conf/compgeom/DeyFW14 and the Compressed Annotation Matrix implementation of \cite DBLP:conf/esa/BoissonnatDM13 diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp index 87e9c207..410cd987 100644 --- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp +++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp @@ -86,9 +86,6 @@ int main(int argc, char **argv) { " - " << simplex.num_simplices() << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; - // Sort the simplices in the order of the filtration - simplex.initialize_filtration(); - std::clog << "Simplex_tree dim: " << simplex.dimension() << std::endl; Persistent_cohomology pcoh(simplex); diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp index 79108730..38c44514 100644 --- a/src/Persistent_cohomology/example/persistence_from_file.cpp +++ b/src/Persistent_cohomology/example/persistence_from_file.cpp @@ -59,9 +59,6 @@ int main(int argc, char * argv[]) { std::clog << std::endl; }*/ - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - // Compute the persistence diagram of the complex Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree); // initializes the coefficient field for homology diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp index 4d329020..236b67de 100644 --- a/src/Persistent_cohomology/example/plain_homology.cpp +++ b/src/Persistent_cohomology/example/plain_homology.cpp @@ -59,9 +59,6 @@ int main() { st.insert_simplex_and_subfaces(edge35); st.insert_simplex(vertex4); - // Sort the simplices in the order of the filtration - st.initialize_filtration(); - // Class for homology computation // By default, since the complex has dimension 1, only 0-dimensional homology would be computed. // Here we also want persistent homology to be computed for the maximal dimension in the complex (persistence_dim_max = true) diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp index e2e2c0a5..2edf5bc4 100644 --- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -59,9 +59,6 @@ int main(int argc, char * argv[]) { std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; std::clog << " 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 diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp index 7da9f15d..a503d983 100644 --- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp @@ -76,9 +76,6 @@ int main(int argc, char * argv[]) { std::clog << "The complex contains " << st.num_simplices() << " simplices \n"; std::clog << " and has dimension " << st.dimension() << " \n"; - // Sort the simplices in the order of the filtration - st.initialize_filtration(); - // Compute the persistence diagram of the complex Persistent_cohomology pcoh(st); // initializes the coefficient field for homology diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp index db456f70..8c5742aa 100644 --- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp @@ -17,10 +17,6 @@ #include <boost/program_options.hpp> -#ifdef GUDHI_USE_TBB -#include <tbb/task_scheduler_init.h> -#endif - #include <string> #include <vector> @@ -67,11 +63,6 @@ int main(int argc, char * argv[]) { std::clog << "The complex contains " << st.num_simplices() << " simplices \n"; std::clog << " and has dimension " << st.dimension() << " \n"; -#ifdef GUDHI_USE_TBB - // Unnecessary, but clarifies which operations are parallel. - tbb::task_scheduler_init ts; -#endif - // Sort the simplices in the order of the filtration st.initialize_filtration(); int count = 0; @@ -81,10 +72,6 @@ int main(int argc, char * argv[]) { // Convert to a more convenient representation. Gudhi::Hasse_complex<> hcpx(st); -#ifdef GUDHI_USE_TBB - ts.terminate(); -#endif - // Free some space. delete &st; diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index ca4bc10d..d34ee07d 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -561,7 +561,6 @@ class Persistent_cohomology { void output_diagram(std::ostream& ostream = std::cout) { cmp_intervals_by_length cmp(cpx_); std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp); - bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity; for (auto pair : persistent_pairs_) { ostream << get<2>(pair) << " " << cpx_->dimension(get<0>(pair)) << " " << cpx_->filtration(get<0>(pair)) << " " @@ -571,9 +570,9 @@ class Persistent_cohomology { void write_output_diagram(std::string diagram_name) { std::ofstream diagram_out(diagram_name.c_str()); + diagram_out.exceptions(diagram_out.failbit); cmp_intervals_by_length cmp(cpx_); std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp); - bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity; for (auto pair : persistent_pairs_) { diagram_out << cpx_->dimension(get<0>(pair)) << " " << cpx_->filtration(get<0>(pair)) << " " |