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+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+from libc.stdint cimport intptr_t
+import os
+
+from gudhi.simplex_tree cimport *
+from gudhi.simplex_tree import SimplexTree
+
+""" 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__ = "GPL v3"
+
+cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
+ cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface":
+ Alpha_complex_interface(vector[vector[double]] points)
+ # bool from_file is a workaround for cython to find the correct signature
+ Alpha_complex_interface(string off_file, bool from_file)
+ vector[double] get_point(int vertex)
+ void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+
+# 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=''):
+ """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
+ """
+
+ # The real cython constructor
+ def __cinit__(self, points=None, off_file=''):
+ if off_file is not '':
+ if os.path.isfile(off_file):
+ self.thisptr = new Alpha_complex_interface(str.encode(off_file), True)
+ else:
+ print("file " + off_file + " not found.")
+ else:
+ if points is None:
+ # Empty Alpha construction
+ points=[]
+ self.thisptr = new Alpha_complex_interface(points)
+
+
+ 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_point(self, vertex):
+ """This function returns the point corresponding to a given vertex.
+
+ :param vertex: The vertex.
+ :type vertex: int
+ :rtype: list of float
+ :returns: the point.
+ """
+ cdef vector[double] point = self.thisptr.get_point(vertex)
+ return point
+
+ def create_simplex_tree(self, max_alpha_square=float('inf')):
+ """
+ :param max_alpha_square: The maximum alpha square threshold the
+ simplices shall not exceed. Default is set to infinity, and
+ there is very little point using anything else since it does
+ not save time.
+ :type max_alpha_square: float
+ :returns: A simplex tree created from the Delaunay Triangulation.
+ :rtype: SimplexTree
+ """
+ stree = SimplexTree()
+ cdef intptr_t stree_int_ptr=stree.thisptr
+ cdef Simplex_tree_interface_full_featured* stree_ptr = <Simplex_tree_interface_full_featured*>stree_int_ptr
+ self.thisptr.create_simplex_tree(stree_ptr, max_alpha_square)
+ return stree