diff options
Diffstat (limited to 'src/python/gudhi/simplex_tree.pxd')
| -rw-r--r-- | src/python/gudhi/simplex_tree.pxd | 118 |
1 files changed, 79 insertions, 39 deletions
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 5f86cfe2..5309c6fa 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -1,19 +1,18 @@ +# This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. +# See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. +# Author(s): Vincent Rouvreau +# +# Copyright (C) 2016 Inria +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair from libcpp cimport bool from libcpp.string cimport string -""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. - See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. - Author(s): Vincent Rouvreau - - Copyright (C) 2016 Inria - - Modification(s): - - YYYY/MM Author: Description of the modification -""" - __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" @@ -22,35 +21,76 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_options_full_featured: pass + cdef cppclass Simplex_tree_simplex_handle "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Simplex_handle": + pass + + cdef cppclass Simplex_tree_simplices_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Complex_simplex_iterator": + Simplex_tree_simplices_iterator() nogil + Simplex_tree_simplex_handle& operator*() nogil + Simplex_tree_simplices_iterator operator++() nogil + bint operator!=(Simplex_tree_simplices_iterator) nogil + + cdef cppclass Simplex_tree_skeleton_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Skeleton_simplex_iterator": + Simplex_tree_skeleton_iterator() nogil + Simplex_tree_simplex_handle& operator*() nogil + Simplex_tree_skeleton_iterator operator++() nogil + bint operator!=(Simplex_tree_skeleton_iterator) nogil + + cdef cppclass Simplex_tree_boundary_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Boundary_simplex_iterator": + Simplex_tree_boundary_iterator() nogil + Simplex_tree_simplex_handle& operator*() nogil + Simplex_tree_boundary_iterator operator++() nogil + bint operator!=(Simplex_tree_boundary_iterator) nogil + + cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>": - Simplex_tree() - double simplex_filtration(vector[int] simplex) - void assign_simplex_filtration(vector[int] simplex, double filtration) - void initialize_filtration() - int num_vertices() - int num_simplices() - void set_dimension(int dimension) - int dimension() - int upper_bound_dimension() - bool find_simplex(vector[int] simplex) - bool insert_simplex_and_subfaces(vector[int] simplex, - double filtration) - vector[pair[vector[int], double]] get_filtration() - vector[pair[vector[int], double]] get_skeleton(int dimension) - vector[pair[vector[int], double]] get_star(vector[int] simplex) - vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, - int dimension) - void expansion(int max_dim) - void remove_maximal_simplex(vector[int] simplex) - bool prune_above_filtration(double filtration) - bool make_filtration_non_decreasing() + Simplex_tree_interface_full_featured() nogil + Simplex_tree_interface_full_featured(Simplex_tree_interface_full_featured&) nogil + double simplex_filtration(vector[int] simplex) nogil + void assign_simplex_filtration(vector[int] simplex, double filtration) nogil + void initialize_filtration() nogil + int num_vertices() nogil + int num_simplices() nogil + void set_dimension(int dimension) nogil + int dimension() nogil + int upper_bound_dimension() nogil + bool find_simplex(vector[int] simplex) nogil + bool insert(vector[int] simplex, double filtration) nogil + void insert_matrix(double* filtrations, int n, int stride0, int stride1, double max_filtration) nogil except + + void insert_batch_vertices(vector[int] v, double f) nogil except + + vector[pair[vector[int], double]] get_star(vector[int] simplex) nogil + vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, int dimension) nogil + void expansion(int max_dim) nogil except + + void remove_maximal_simplex(vector[int] simplex) nogil + bool prune_above_filtration(double filtration) nogil + bool make_filtration_non_decreasing() nogil + void compute_extended_filtration() nogil + Simplex_tree_interface_full_featured* collapse_edges(int nb_collapse_iteration) nogil except + + void reset_filtration(double filtration, int dimension) nogil + bint operator==(Simplex_tree_interface_full_featured) nogil + # Iterators over Simplex tree + pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex) nogil + Simplex_tree_simplices_iterator get_simplices_iterator_begin() nogil + Simplex_tree_simplices_iterator get_simplices_iterator_end() nogil + vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_begin() nogil + vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end() nogil + Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil + Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil + pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] get_boundary_iterators(vector[int] simplex) nogil except + + # Expansion with blockers + ctypedef bool (*blocker_func_t)(vector[int], void *user_data) + void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data) cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": - cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>": - Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max) - vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence) - vector[int] betti_numbers() - vector[int] persistent_betti_numbers(double from_value, double to_value) - vector[pair[double,double]] intervals_in_dimension(int dimension) - void write_output_diagram(string diagram_file_name) - vector[pair[vector[int], vector[int]]] persistence_pairs() + cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>>": + Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max) nogil + void compute_persistence(int homology_coeff_field, double min_persistence) nogil except + + vector[pair[int, pair[double, double]]] get_persistence() nogil + vector[int] betti_numbers() nogil + vector[int] persistent_betti_numbers(double from_value, double to_value) nogil + vector[pair[double,double]] intervals_in_dimension(int dimension) nogil + void write_output_diagram(string diagram_file_name) nogil except + + vector[pair[vector[int], vector[int]]] persistence_pairs() nogil + pair[vector[vector[int]], vector[vector[int]]] lower_star_generators() nogil + pair[vector[vector[int]], vector[vector[int]]] flag_generators() nogil + vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(double min_persistence) nogil |