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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 "Cubical_complex_interface.h" namespace "Gudhi":
cdef cppclass Periodic_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>":
Periodic_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells, vector[bool] periodic_dimensions)
Periodic_cubical_complex_base_interface(string perseus_file)
int num_simplices()
int dimension()
cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
cdef cppclass Periodic_cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>>":
Periodic_cubical_complex_persistence_interface(Periodic_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)
# PeriodicCubicalComplex python interface
cdef class PeriodicCubicalComplex:
"""The PeriodicCubicalComplex is an example of a structured complex useful
in computational mathematics (specially rigorous numerics) and image
analysis.
"""
cdef Periodic_cubical_complex_base_interface * thisptr
cdef Periodic_cubical_complex_persistence_interface * pcohptr
# Fake constructor that does nothing but documenting the constructor
def __init__(self, dimensions=None, top_dimensional_cells=None,
periodic_dimensions=None, perseus_file=''):
"""PeriodicCubicalComplex 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
:param periodic_dimensions: A list of top dimensional cells periodicity value.
:type periodic_dimensions: list of boolean
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,
periodic_dimensions=None, perseus_file=''):
if (dimensions is not None) and (top_dimensional_cells is not None) and (periodic_dimensions is not None) and (perseus_file is ''):
self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells, periodic_dimensions)
elif (dimensions is None) and (top_dimensional_cells is None) and (periodic_dimensions is None) and (perseus_file is not ''):
if os.path.isfile(perseus_file):
self.thisptr = new Periodic_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 PeriodicCubicalComplex 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 Periodic_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
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