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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
import os
""" 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"
cdef extern from "Rips_complex_interface.h" namespace "Gudhi":
cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface":
Rips_complex_interface()
void init_points(vector[vector[double]] values, double threshold)
void init_matrix(vector[vector[double]] values, double threshold)
void init_points_sparse(vector[vector[double]] values, double threshold, double sparse)
void init_matrix_sparse(vector[vector[double]] values, double threshold, double sparse)
void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max)
# RipsComplex python interface
cdef class RipsComplex:
"""The data structure is a one skeleton graph, or Rips graph, containing
edges when the edge length is less or equal to a given threshold. Edge
length is computed from a user given point cloud with a given distance
function, or a distance matrix.
"""
cdef Rips_complex_interface thisref
# Fake constructor that does nothing but documenting the constructor
def __init__(self, points=None, distance_matrix=None,
max_edge_length=float('inf'), sparse=None):
"""RipsComplex constructor.
:param max_edge_length: Rips value.
:type max_edge_length: float
:param points: A list of points in d-Dimension.
:type points: list of list of double
Or
:param distance_matrix: A distance matrix (full square or lower
triangular).
:type points: list of list of double
And in both cases
:param sparse: If this is not None, it switches to building a sparse
Rips and represents the approximation parameter epsilon.
:type sparse: float
"""
# The real cython constructor
def __cinit__(self, points=None, distance_matrix=None,
max_edge_length=float('inf'), sparse=None):
if sparse is not None:
if distance_matrix is not None:
self.thisref.init_matrix_sparse(distance_matrix,
max_edge_length,
sparse)
else:
if points is None:
# Empty Rips construction
points=[]
self.thisref.init_points_sparse(points, max_edge_length, sparse)
else:
if distance_matrix is not None:
self.thisref.init_matrix(distance_matrix, max_edge_length)
else:
if points is None:
# Empty Rips construction
points=[]
self.thisref.init_points(points, max_edge_length)
def create_simplex_tree(self, max_dimension=1):
"""
:param max_dimension: graph expansion for rips until this given maximal
dimension.
:type max_dimension: int
:returns: A simplex tree created from the Delaunay Triangulation.
:rtype: SimplexTree
"""
simplex_tree = SimplexTree()
self.thisref.create_simplex_tree(simplex_tree.thisptr, max_dimension)
return simplex_tree
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