diff options
Diffstat (limited to 'cython/cython/simplex_tree.pyx')
| -rw-r--r-- | cython/cython/simplex_tree.pyx | 45 |
1 files changed, 43 insertions, 2 deletions
diff --git a/cython/cython/simplex_tree.pyx b/cython/cython/simplex_tree.pyx index 0cb575d2..e302486b 100644 --- a/cython/cython/simplex_tree.pyx +++ b/cython/cython/simplex_tree.pyx @@ -10,7 +10,7 @@ from libcpp.string cimport string Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria 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 @@ -27,7 +27,7 @@ from libcpp.string cimport string """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": @@ -55,6 +55,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": void expansion(int max_dim) void remove_maximal_simplex(vector[int] simplex) bool prune_above_filtration(double filtration) + bool make_filtration_non_decreasing() 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>>": @@ -64,6 +65,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": 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() # SimplexTree python interface cdef class SimplexTree: @@ -399,6 +401,26 @@ cdef class SimplexTree: """ self.thisptr.expansion(max_dim) + def make_filtration_non_decreasing(self): + """This function ensures that each simplex has a higher filtration + value than its faces by increasing the filtration values. + + :returns: The filtration modification information. + :rtype: bint + + + .. note:: + + Some simplex tree functions require the filtration to be valid. + make_filtration_non_decreasing function is not launching + :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>` + but returns the filtration modification + information. If the complex has changed , please call + :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>` + to recompute it. + """ + return self.thisptr.make_filtration_non_decreasing() + def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False): """This function returns the persistence of the simplicial complex. @@ -486,6 +508,25 @@ cdef class SimplexTree: " to be launched first.") return intervals_result + def persistence_pairs(self): + """This function returns the persistence pairs of the simplicial + complex. + + :returns: The persistence intervals. + :rtype: list of pair of list of int + + :note: intervals_in_dim function requires + :func:`persistence()<gudhi.SimplexTree.persistence>` + function to be launched first. + """ + cdef vector[pair[vector[int],vector[int]]] persistence_pairs_result + if self.pcohptr != NULL: + persistence_pairs_result = self.pcohptr.persistence_pairs() + else: + print("persistence_pairs function requires persistence function" + " to be launched first.") + return persistence_pairs_result + def write_persistence_diagram(self, persistence_file=''): """This function writes the persistence intervals of the simplicial complex in a user given file name. |