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Diffstat (limited to 'src/cython/cython/alpha_complex.pyx')
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diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx new file mode 100644 index 00000000..af609863 --- /dev/null +++ b/src/cython/cython/alpha_complex.pyx @@ -0,0 +1,363 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp.string cimport string +from libcpp cimport bool +import os + +"""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) 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 + 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/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": + cdef cppclass Alpha_complex_interface "Gudhi::alphacomplex::Alpha_complex_interface": + Alpha_complex_interface(vector[vector[double]] points, double max_alpha_square) + # bool from_file is a workaround for cython to find the correct signature + Alpha_complex_interface(string off_file, double max_alpha_square, bool from_file) + double filtration() + double simplex_filtration(vector[int] simplex) + void set_filtration(double filtration) + void initialize_filtration() + int num_vertices() + int num_simplices() + void set_dimension(int dimension) + int dimension() + bint find_simplex(vector[int] simplex) + bint insert_simplex_and_subfaces(vector[int] simplex, + double filtration) + vector[pair[vector[int], double]] get_filtered_tree() + vector[pair[vector[int], double]] get_skeleton_tree(int dimension) + vector[pair[vector[int], double]] get_star_tree(vector[int] simplex) + vector[pair[vector[int], double]] get_coface_tree(vector[int] simplex, + int dimension) + void remove_maximal_simplex(vector[int] simplex) + vector[double] get_point(int vertex) + vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence) + vector[int] get_betti_numbers() + vector[int] get_persistent_betti_numbers(double from_value, double to_value) + +# AlphaComplex python interface +cdef class AlphaComplex: + """AlphaComplex is a simplicial complex constructed from the finite cells + of a Delaunay Triangulation. + + The filtration value of each simplex is computed as the square of the + circumradius of the simplex if the circumsphere is empty (the simplex is + then said to be Gabriel), and as the minimum of the filtration values of + the codimension 1 cofaces that make it not Gabriel otherwise. + + All simplices that have a filtration value strictly greater than a given + alpha squared value are not inserted into the complex. + + .. note:: + + When Alpha_complex is constructed with an infinite value of alpha, the + complex is a Delaunay complex. + + """ + + cdef Alpha_complex_interface * thisptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, points=None, off_file='', max_alpha_square=float('inf')): + """AlphaComplex constructor. + + :param points: A list of points in d-Dimension. + :type points: list of list of double + + Or + + :param off_file: An OFF file style name. + :type off_file: string + + :param max_alpha_square: Maximum Alpha square value. Default is :math:`\infty` + :type max_alpha_square: double + """ + + # The real cython constructor + def __cinit__(self, points=[], off_file='', max_alpha_square=float('inf')): + if off_file is not '': + if os.path.isfile(off_file): + self.thisptr = new Alpha_complex_interface(off_file, + max_alpha_square, True) + else: + print("file " + off_file + " not found.") + else: + self.thisptr = new Alpha_complex_interface(points, + max_alpha_square) + + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + + def __is_defined(self): + """Returns true if AlphaComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def get_filtration(self): + """This function returns the main simplicial complex filtration value. + + :returns: float -- the simplicial complex filtration value. + """ + return self.thisptr.filtration() + + def filtration(self, simplex): + """This function returns the simplicial complex filtration value for a + given N-simplex. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int + :returns: float -- the simplicial complex filtration value. + """ + return self.thisptr.simplex_filtration(simplex) + + def set_filtration(self, filtration): + """This function sets the main simplicial complex filtration value. + + :param filtration: The filtration value. + :type filtration: float. + """ + self.thisptr.set_filtration(<double> filtration) + + def initialize_filtration(self): + """This function initializes and sorts the simplicial complex + filtration vector. + + .. note:: + + This function must be launched before persistence, betti_numbers, + persistent_betti_numbers or get_filtered_tree after inserting or + removing simplices. + """ + self.thisptr.initialize_filtration() + + def num_vertices(self): + """This function returns the number of vertices of the simplicial + complex. + + :returns: int -- the simplicial complex number of vertices. + """ + return self.thisptr.num_vertices() + + def num_simplices(self): + """This function returns the number of simplices of the simplicial + complex. + + :returns: int -- the simplicial complex number of simplices. + """ + return self.thisptr.num_simplices() + + def dimension(self): + """This function returns the dimension of the simplicial complex. + + :returns: int -- the simplicial complex dimension. + """ + return self.thisptr.dimension() + + def set_dimension(self, dimension): + """This function sets the dimension of the simplicial complex. + + :param dimension: The new dimension value. + :type dimension: int. + """ + self.thisptr.set_dimension(<int>dimension) + + def find(self, simplex): + """This function returns if the N-simplex was found in the simplicial + complex or not. + + :param simplex: The N-simplex to find, represented by a list of vertex. + :type simplex: list of int. + :returns: bool -- true if the simplex was found, false otherwise. + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + return self.thisptr.find_simplex(complex) + + def insert(self, simplex, filtration=0.0): + """This function inserts the given N-simplex with the given filtration + value (default value is '0.0'). + + :param simplex: The N-simplex to insert, represented by a list of + vertex. + :type simplex: list of int. + :param filtration: The filtration value of the simplex. + :type filtration: float. + :returns: bool -- true if the simplex was found, false otherwise. + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + return self.thisptr.insert_simplex_and_subfaces(complex, + <double>filtration) + + def get_filtered_tree(self): + """This function returns the tree sorted by increasing filtration + values. + + :returns: list of tuples(simplex, filtration) -- the tree sorted by + increasing filtration values. + """ + cdef vector[pair[vector[int], double]] coface_tree \ + = self.thisptr.get_filtered_tree() + ct = [] + for filtered_complex in coface_tree: + v = [] + for vertex in filtered_complex.first: + v.append(vertex) + ct.append((v, filtered_complex.second)) + return ct + + def get_skeleton_tree(self, dimension): + """This function returns the tree skeleton of a maximum given + dimension. + + :param dimension: The skeleton dimension value. + :type dimension: int. + :returns: list of tuples(simplex, filtration) -- the skeleton tree + of a maximum dimension. + """ + cdef vector[pair[vector[int], double]] coface_tree \ + = self.thisptr.get_skeleton_tree(<int>dimension) + ct = [] + for filtered_complex in coface_tree: + v = [] + for vertex in filtered_complex.first: + v.append(vertex) + ct.append((v, filtered_complex.second)) + return ct + + def get_star_tree(self, simplex): + """This function returns the star tree of a given N-simplex. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + :returns: list of tuples(simplex, filtration) -- the star tree of a + simplex. + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + cdef vector[pair[vector[int], double]] coface_tree \ + = self.thisptr.get_star_tree(complex) + ct = [] + for filtered_complex in coface_tree: + v = [] + for vertex in filtered_complex.first: + v.append(vertex) + ct.append((v, filtered_complex.second)) + return ct + + def get_coface_tree(self, simplex, codimension): + """This function returns the coface tree of a given N-simplex with a + given codimension. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + :param codimension: The codimension. If codimension = 0, all cofaces + are returned (equivalent of get_star_tree function) + :type codimension: int. + :returns: list of tuples(simplex, filtration) -- the coface tree of a + simplex. + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + cdef vector[pair[vector[int], double]] coface_tree \ + = self.thisptr.get_coface_tree(complex, <int>codimension) + ct = [] + for filtered_complex in coface_tree: + v = [] + for vertex in filtered_complex.first: + v.append(vertex) + ct.append((v, filtered_complex.second)) + return ct + + def remove_maximal_simplex(self, simplex): + """This function removes a given maximal N-simplex from the simplicial + complex. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + """ + self.thisptr.remove_maximal_simplex(simplex) + + def get_point(self, vertex): + """This function returns the point corresponding to a given vertex. + + :param vertex: The vertex. + :type vertex: int. + :returns: list of float -- the point. + """ + cdef vector[double] point = self.thisptr.get_point(vertex) + return point + + def persistence(self, homology_coeff_field=11, min_persistence=0.0): + """This function returns the persistence of the simplicial complex. + + :param homology_coeff_field: The homology coefficient field. Must be a + prime number + :type homology_coeff_field: int. + :param min_persistence: The minimum persistence value to take into + account (strictly greater than min_persistence). Default value is + 0.0. + Sets min_persistence to -1.0 to see all values. + :type min_persistence: float. + :note: list of pairs(dimension, pair(birth, death)) -- the + persistence of the simplicial complex. + """ + return self.thisptr.get_persistence(homology_coeff_field, min_persistence) + + def betti_numbers(self): + """This function returns the Betti numbers of the simplicial complex. + + :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]). + + :note: betti_numbers function requires persistence function to be + launched first. + """ + return self.thisptr.get_betti_numbers() + + def persistent_betti_numbers(self, from_value, to_value): + """This function returns the persistent Betti numbers of the + simplicial complex. + + :param from_value: The persistence birth limit to be added in the + numbers (persistent birth <= from_value). + :type from_value: float. + :param to_value: The persistence death limit to be added in the + numbers (persistent death > to_value). + :type to_value: float. + + :returns: list of int -- The persistent Betti numbers ([B0, B1, ..., + Bn]). + + :note: persistent_betti_numbers function requires persistence + function to be launched first. + """ + return self.thisptr.get_persistent_betti_numbers(from_value, to_value) |