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Diffstat (limited to 'cython/cython/cubical_complex.pyx')
| -rw-r--r-- | cython/cython/cubical_complex.pyx | 198 |
1 files changed, 0 insertions, 198 deletions
diff --git a/cython/cython/cubical_complex.pyx b/cython/cython/cubical_complex.pyx deleted file mode 100644 index e94cd539..00000000 --- a/cython/cython/cubical_complex.pyx +++ /dev/null @@ -1,198 +0,0 @@ -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 "Cubical_complex_interface.h" namespace "Gudhi": - cdef cppclass Bitmap_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface<>": - Bitmap_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells) - Bitmap_cubical_complex_base_interface(string perseus_file) - int num_simplices() - int dimension() - -cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": - cdef cppclass Cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<>>": - Cubical_complex_persistence_interface(Bitmap_cubical_complex_base_interface * st, bool persistence_dim_max) - vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence) - vector[int] betti_numbers() - vector[int] persistent_betti_numbers(double from_value, double to_value) - vector[pair[double,double]] intervals_in_dimension(int dimension) - -# CubicalComplex python interface -cdef class CubicalComplex: - """The CubicalComplex is an example of a structured complex useful in - computational mathematics (specially rigorous numerics) and image - analysis. - """ - cdef Bitmap_cubical_complex_base_interface * thisptr - - cdef Cubical_complex_persistence_interface * pcohptr - - # Fake constructor that does nothing but documenting the constructor - def __init__(self, dimensions=None, top_dimensional_cells=None, - perseus_file=''): - """CubicalComplex constructor from dimensions and - top_dimensional_cells or from a Perseus-style file name. - - :param dimensions: A list of number of top dimensional cells. - :type dimensions: list of int - :param top_dimensional_cells: A list of cells filtration values. - :type top_dimensional_cells: list of double - - Or - - :param perseus_file: A Perseus-style file name. - :type perseus_file: string - """ - - # The real cython constructor - def __cinit__(self, dimensions=None, top_dimensional_cells=None, - perseus_file=''): - if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''): - self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells) - elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''): - if os.path.isfile(perseus_file): - self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file)) - else: - print("file " + perseus_file + " not found.") - else: - print("CubicalComplex can be constructed from dimensions and " - "top_dimensional_cells or from a Perseus-style file name.") - - def __dealloc__(self): - if self.thisptr != NULL: - del self.thisptr - if self.pcohptr != NULL: - del self.pcohptr - - def __is_defined(self): - """Returns true if CubicalComplex pointer is not NULL. - """ - return self.thisptr != NULL - - def __is_persistence_defined(self): - """Returns true if Persistence pointer is not NULL. - """ - return self.pcohptr != NULL - - def num_simplices(self): - """This function returns the number of all cubes in the complex. - - :returns: int -- the number of all cubes in the complex. - """ - return self.thisptr.num_simplices() - - def dimension(self): - """This function returns the dimension of the complex. - - :returns: int -- the complex dimension. - """ - return self.thisptr.dimension() - - def persistence(self, homology_coeff_field=11, min_persistence=0): - """This function returns the persistence of the complex. - - :param homology_coeff_field: The homology coefficient field. Must be a - prime number - :type homology_coeff_field: int. - :param min_persistence: The minimum persistence value to take into - account (strictly greater than min_persistence). Default value is - 0.0. - Sets min_persistence to -1.0 to see all values. - :type min_persistence: float. - :returns: list of pairs(dimension, pair(birth, death)) -- the - persistence of the complex. - """ - if self.pcohptr != NULL: - del self.pcohptr - if self.thisptr != NULL: - self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr, True) - cdef vector[pair[int, pair[double, double]]] persistence_result - if self.pcohptr != NULL: - persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) - return persistence_result - - def betti_numbers(self): - """This function returns the Betti numbers of the complex. - - :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]). - - :note: betti_numbers function requires persistence function to be - launched first. - - :note: betti_numbers function always returns [1, 0, 0, ...] as infinity - filtration cubes are not removed from the complex. - """ - cdef vector[int] bn_result - if self.pcohptr != NULL: - bn_result = self.pcohptr.betti_numbers() - return bn_result - - def persistent_betti_numbers(self, from_value, to_value): - """This function returns the persistent Betti numbers of the complex. - - :param from_value: The persistence birth limit to be added in the - numbers (persistent birth <= from_value). - :type from_value: float. - :param to_value: The persistence death limit to be added in the - numbers (persistent death > to_value). - :type to_value: float. - - :returns: list of int -- The persistent Betti numbers ([B0, B1, ..., - Bn]). - - :note: persistent_betti_numbers function requires persistence - function to be launched first. - """ - cdef vector[int] pbn_result - if self.pcohptr != NULL: - pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value) - return pbn_result - - def persistence_intervals_in_dimension(self, dimension): - """This function returns the persistence intervals of the complex in a - specific dimension. - - :param dimension: The specific dimension. - :type from_value: int. - :returns: The persistence intervals. - :rtype: list of pair of float - - :note: intervals_in_dim function requires persistence function to be - launched first. - """ - cdef vector[pair[double,double]] intervals_result - if self.pcohptr != NULL: - intervals_result = self.pcohptr.intervals_in_dimension(dimension) - else: - print("intervals_in_dim function requires persistence function" - " to be launched first.") - return intervals_result |