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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 "Tangential_complex_interface.h" namespace "Gudhi":
cdef cppclass Tangential_complex_interface "Gudhi::tangential_complex::Tangential_complex_interface":
Tangential_complex_interface(int intrisic_dim, vector[vector[double]] points)
# bool from_file is a workaround for cython to find the correct signature
Tangential_complex_interface(int intrisic_dim, string off_file, bool from_file)
vector[double] get_point(unsigned vertex)
unsigned number_of_vertices()
unsigned number_of_simplices()
unsigned number_of_inconsistent_simplices()
unsigned number_of_inconsistent_stars()
void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree)
void fix_inconsistencies_using_perturbation(double max_perturb, double time_limit)
# TangentialComplex python interface
cdef class TangentialComplex:
"""The class Tangential_complex represents a tangential complex. After the
computation of the complex, an optional post-processing called perturbation
can be run to attempt to remove inconsistencies.
"""
cdef Tangential_complex_interface * thisptr
# Fake constructor that does nothing but documenting the constructor
def __init__(self, intrisic_dim, points=None, off_file=''):
"""TangentialComplex constructor.
:param intrisic_dim: Intrinsic dimension of the manifold.
:type intrisic_dim: integer
: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, intrisic_dim, points=None, off_file=''):
if off_file is not '':
if os.path.isfile(off_file):
self.thisptr = new Tangential_complex_interface(intrisic_dim, str.encode(off_file), True)
else:
print("file " + off_file + " not found.")
else:
if points is None:
# Empty tangential construction
points=[]
self.thisptr = new Tangential_complex_interface(intrisic_dim, points)
def __dealloc__(self):
if self.thisptr != NULL:
del self.thisptr
def __is_defined(self):
"""Returns true if TangentialComplex 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.
:returns: The point.
:rtype: list of float
"""
cdef vector[double] point = self.thisptr.get_point(vertex)
return point
def num_vertices(self):
"""
:returns: The number of vertices.
:rtype: unsigned
"""
return self.thisptr.number_of_vertices()
def num_simplices(self):
"""
:returns: Total number of simplices in stars (including duplicates that appear in several stars).
:rtype: unsigned
"""
return self.thisptr.number_of_simplices()
def num_inconsistent_simplices(self):
"""
:returns: The number of inconsistent simplices.
:rtype: unsigned
"""
return self.thisptr.number_of_inconsistent_simplices()
def num_inconsistent_stars(self):
"""
:returns: The number of stars containing at least one inconsistent simplex.
:rtype: unsigned
"""
return self.thisptr.number_of_inconsistent_stars()
def create_simplex_tree(self):
"""Exports the complex into a simplex tree.
:returns: A simplex tree created from the complex.
:rtype: SimplexTree
"""
simplex_tree = SimplexTree()
self.thisptr.create_simplex_tree(simplex_tree.thisptr)
return simplex_tree
def fix_inconsistencies_using_perturbation(self, max_perturb, time_limit=-1.0):
"""Attempts to fix inconsistencies by perturbing the point positions.
:param max_perturb: Maximum length of the translations used by the
perturbation.
:type max_perturb: double
:param time_limit: Time limit in seconds. If -1, no time limit is set.
:type time_limit: double
"""
self.thisptr.fix_inconsistencies_using_perturbation(max_perturb,
time_limit)
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