diff options
Diffstat (limited to 'cython/cython/tangential_complex.pyx')
-rw-r--r-- | cython/cython/tangential_complex.pyx | 151 |
1 files changed, 151 insertions, 0 deletions
diff --git a/cython/cython/tangential_complex.pyx b/cython/cython/tangential_complex.pyx new file mode 100644 index 00000000..d55bb050 --- /dev/null +++ b/cython/cython/tangential_complex.pyx @@ -0,0 +1,151 @@ +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(vector[vector[double]] points) + # bool from_file is a workaround for cython to find the correct signature + Tangential_complex_interface(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, points=None, off_file=''): + """TangentialComplex 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 Tangential_complex_interface(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(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) |