diff options
12 files changed, 30 insertions, 32 deletions
diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp index 6e9be97b..fd9f0858 100644 --- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp +++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp @@ -56,7 +56,7 @@ void program_options(int argc, char * argv[] , int & p , Filtration_value & min_persistence); -static inline std::pair<double, double> compute_root_square (std::pair<double, double> input) { +static inline std::pair<double, double> compute_root_square(std::pair<double, double> input) { return std::make_pair(std::sqrt(input.first), std::sqrt(input.second)); } diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h index 076f1be0..e7dafaa0 100644 --- a/src/Contraction/example/Garland_heckbert/Error_quadric.h +++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h @@ -21,8 +21,8 @@ * */ -#ifndef ERROR_QUADRIC_H_ -#define ERROR_QUADRIC_H_ +#ifndef GARLAND_HECKBERT_ERROR_QUADRIC_H_ +#define GARLAND_HECKBERT_ERROR_QUADRIC_H_ #include <boost/optional/optional.hpp> @@ -179,4 +179,4 @@ template <typename Point> class Error_quadric { } }; -#endif // ERROR_QUADRIC_H_ +#endif // GARLAND_HECKBERT_ERROR_QUADRIC_H_ diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h index ceefd2ba..7865e4ec 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h +++ b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef EXAMPLE_PERSISTENT_COHOMOLOGY_ALPHA_COMPLEX_3D_HELPER_H_ -#define EXAMPLE_PERSISTENT_COHOMOLOGY_ALPHA_COMPLEX_3D_HELPER_H_ +#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) { @@ -73,4 +73,4 @@ Vertex_list from_vertex(const Vertex_handle& vh) { return the_list; } -#endif // EXAMPLE_PERSISTENT_COHOMOLOGY_ALPHA_COMPLEX_3D_HELPER_H_ +#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 index ffb98283..40f4aff9 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -20,6 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include "alpha_complex_3d_helper.h" + #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_3D_off_io.h> @@ -30,8 +32,6 @@ #include <CGAL/Alpha_shape_3.h> #include <CGAL/iterator.h> -#include "alpha_complex_3d_helper.h" - #include <fstream> #include <cmath> #include <string> 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 c016a596..70054601 100644 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -20,6 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include "alpha_complex_3d_helper.h" + #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_3D_off_io.h> @@ -30,8 +32,6 @@ #include <CGAL/Alpha_shape_3.h> #include <CGAL/iterator.h> -#include "alpha_complex_3d_helper.h" - #include <fstream> #include <cmath> #include <string> diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp index 4f6ea40e..28f563aa 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -20,6 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include "alpha_complex_3d_helper.h" + #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_3D_off_io.h> @@ -31,8 +33,6 @@ #include <CGAL/Alpha_shape_3.h> #include <CGAL/iterator.h> -#include "alpha_complex_3d_helper.h" - #include <fstream> #include <cmath> #include <string> diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp index ae82c817..50f692f2 100644 --- a/src/Persistent_cohomology/example/plain_homology.cpp +++ b/src/Persistent_cohomology/example/plain_homology.cpp @@ -27,13 +27,11 @@ #include <vector> #include <cstdint> // for std::uint8_t -using namespace Gudhi; - /* We could perfectly well use the default Simplex_tree<> (which uses * Simplex_tree_options_full_featured), the following simply demonstrates * how to save on storage by not storing a filtration value. */ -struct MyOptions : Simplex_tree_options_full_featured { +struct MyOptions : Gudhi::Simplex_tree_options_full_featured { // Implicitly use 0 as filtration value for all simplices static const bool store_filtration = false; // The persistence algorithm needs this @@ -43,7 +41,10 @@ struct MyOptions : Simplex_tree_options_full_featured { // Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key typedef std::uint8_t Simplex_key; }; -typedef Simplex_tree<MyOptions> ST; + +using ST = Gudhi::Simplex_tree<MyOptions>; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Field_Zp>; int main() { ST st; @@ -70,7 +71,7 @@ int main() { st.initialize_filtration(); // Class for homology computation - persistent_cohomology::Persistent_cohomology<ST, persistent_cohomology::Field_Zp> pcoh(st); + Persistent_cohomology pcoh(st); // Initialize the coefficient field Z/2Z for homology pcoh.init_coefficients(2); 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 5203548a..0b137535 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -20,6 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include "alpha_complex_3d_helper.h" + #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_3D_off_io.h> @@ -31,8 +33,6 @@ #include <CGAL/Alpha_shape_3.h> #include <CGAL/iterator.h> -#include "alpha_complex_3d_helper.h" - #include <fstream> #include <cmath> #include <string> @@ -49,7 +49,7 @@ using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>; using Vb = CGAL::Alpha_shape_vertex_base_3<Gt>; using Fb = CGAL::Alpha_shape_cell_base_3<Gt>; using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>; -using Triangulation_3 = CGAL::Regular_triangulation_3<Gt,Tds>; +using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>; using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>; // From file type definition @@ -115,8 +115,7 @@ int main(int argc, char * const argv[]) { double weight = 0.0; std::size_t index = 0; // Attempt read the weight in a double format, return false if it fails - while((weights_ifstr >> weight) && (index < lp.size())) - { + while ((weights_ifstr >> weight) && (index < lp.size())) { wp.push_back(Weighted_point_3(lp[index], weight)); index++; } diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp index 7e48aaaf..ad99df23 100644 --- a/src/Simplex_tree/example/mini_simplex_tree.cpp +++ b/src/Simplex_tree/example/mini_simplex_tree.cpp @@ -24,19 +24,18 @@ #include <iostream> #include <initializer_list> -using namespace Gudhi; - -struct MyOptions : Simplex_tree_options_full_featured { +struct MyOptions : Gudhi::Simplex_tree_options_full_featured { // Not doing persistence, so we don't need those static const bool store_key = false; static const bool store_filtration = false; // I have few vertices typedef short Vertex_handle; }; -typedef Simplex_tree<MyOptions> ST; + +using ST = Gudhi::Simplex_tree<MyOptions>; // Dictionary should be private, but for now this is the easiest way. -static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Simplex_tree<>::Dictionary::value_type), +static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Gudhi::Simplex_tree<>::Dictionary::value_type), "Not storing the filtration and key should save some space"); int main() { diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index e2791f76..63f03687 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -178,7 +178,7 @@ class Witness_complex { norelax_dist2 = l_it->second; } } else if (dim == 0) { - for (;l_it != end && l_it->second - alpha2 <= norelax_dist2; ++l_it) { + for (; l_it != end && l_it->second - alpha2 <= norelax_dist2; ++l_it) { simplex.push_back(l_it->first); double filtration_value = 0; // if norelax_dist is infinite, relaxation is 0. diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index 7bf97c23..22747637 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -24,8 +24,8 @@ #define DISTANCE_FUNCTIONS_H_ #include <cmath> // for std::sqrt -#include <type_traits> // for std::decay -#include <iterator> // for std::begin, std::end +#include <type_traits> // for std::decay +#include <iterator> // for std::begin, std::end /** @file * @brief Global distance functions diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h index 25c458d2..55028fd0 100644 --- a/src/cython/include/Persistent_cohomology_interface.h +++ b/src/cython/include/Persistent_cohomology_interface.h @@ -88,7 +88,6 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol private: // A copy FilteredComplex* stptr_; - }; } // namespace Gudhi |