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# 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
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
__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)
void compute_tangential_complex() except +
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)
void set_max_squared_edge_length(double max_squared_edge_length)
# 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:
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 compute_tangential_complex(self):
"""This function computes the tangential complex.
Raises:
ValueError: In debug mode, if the computed star dimension is too
low. Try to set a bigger maximal edge length value with
:meth:`set_max_squared_edge_length`
if this happens.
"""
self.thisptr.compute_tangential_complex()
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
"""
stree = SimplexTree()
cdef intptr_t stree_int_ptr=stree.thisptr
self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr)
return stree
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)
def set_max_squared_edge_length(self, max_squared_edge_length):
"""Sets the maximal possible squared edge length for the edges in the
triangulations.
:param max_squared_edge_length: Maximal possible squared edge length.
:type max_squared_edge_length: double
If the maximal edge length value is too low
:meth:`compute_tangential_complex`
will throw an exception in debug mode.
"""
self.thisptr.set_max_squared_edge_length(max_squared_edge_length)
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