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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. 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 "Rips_complex_interface.h" namespace "Gudhi":
+ cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface":
+ Rips_complex_interface(vector[vector[double]] values, double threshold, bool euclidean)
+ # bool from_file is a workaround for cython to find the correct signature
+ Rips_complex_interface(string file_name, double threshold, bool euclidean, bool from_file)
+ 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 * thisptr
+
+ # Fake constructor that does nothing but documenting the constructor
+ def __init__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
+ """RipsComplex constructor.
+
+ :param max_edge_length: Rips value.
+ :type max_edge_length: int
+
+ :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
+
+ Or
+
+ :param distance_matrix: A distance matrix (full square or lower
+ triangular).
+ :type points: list of list of double
+
+ Or
+
+ :param csv_file: A csv file style name containing a full square or a
+ lower triangular distance matrix.
+ :type csv_file: string
+ """
+
+ # The real cython constructor
+ def __cinit__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
+ if off_file is not '':
+ if os.path.isfile(off_file):
+ self.thisptr = new Rips_complex_interface(str.encode(off_file),
+ max_edge_length,
+ True,
+ True)
+ else:
+ print("file " + off_file + " not found.")
+ elif csv_file is not '':
+ if os.path.isfile(csv_file):
+ self.thisptr = new Rips_complex_interface(str.encode(csv_file),
+ max_edge_length,
+ False,
+ True)
+ else:
+ print("file " + csv_file + " not found.")
+ elif distance_matrix is not None:
+ self.thisptr = new Rips_complex_interface(distance_matrix, max_edge_length, False)
+ else:
+ if points is None:
+ # Empty Rips construction
+ points=[]
+ self.thisptr = new Rips_complex_interface(points, max_edge_length, True)
+
+
+ def __dealloc__(self):
+ if self.thisptr != NULL:
+ del self.thisptr
+
+ def __is_defined(self):
+ """Returns true if RipsComplex pointer is not NULL.
+ """
+ return self.thisptr != NULL
+
+ 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.thisptr.create_simplex_tree(simplex_tree.thisptr, max_dimension)
+ return simplex_tree