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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 __future__ import print_function
from cython cimport numeric
from libcpp.vector cimport vector
from libcpp.utility cimport pair
from libcpp.string cimport string
from libcpp cimport bool
import sys
import os
import numpy as np
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
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)
void compute_persistence(int homology_coeff_field, double min_persistence)
vector[pair[int, pair[double, double]]] get_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 top_dimensional_cells: A multidimensional array of cells
filtration values.
:type top_dimensional_cells: anything convertible to a numpy ndarray
: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 == '')):
self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
top_dimensional_cells,
periodic_dimensions)
elif ((dimensions is None) and (top_dimensional_cells is not None)
and (periodic_dimensions is not None) and (perseus_file == '')):
top_dimensional_cells = np.array(top_dimensional_cells,
copy = False,
order = 'F')
dimensions = top_dimensional_cells.shape
top_dimensional_cells = top_dimensional_cells.ravel(order='F')
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 != '')):
if os.path.isfile(perseus_file):
self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file.encode('utf-8'))
else:
print("file " + perseus_file + " not found.", file=sys.stderr)
else:
print("CubicalComplex can be constructed from dimensions, "
"top_dimensional_cells and periodic_dimensions, or from "
"top_dimensional_cells and periodic_dimensions or from "
"a Perseus-style file name.", file=sys.stderr)
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 compute_persistence(self, homology_coeff_field=11, min_persistence=0):
"""This function computes the persistence of the complex, so it can be
accessed through :func:`persistent_betti_numbers`,
:func:`persistence_intervals_in_dimension`, etc. This function is
equivalent to :func:`persistence` when you do not want the list
:func:`persistence` returns.
: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: Nothing.
"""
if self.pcohptr != NULL:
del self.pcohptr
assert self.__is_defined()
self.pcohptr = new Periodic_cubical_complex_persistence_interface(self.thisptr, True)
self.pcohptr.compute_persistence(homology_coeff_field, min_persistence)
def persistence(self, homology_coeff_field=11, min_persistence=0):
"""This function computes and 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.
"""
self.compute_persistence(homology_coeff_field, min_persistence)
return self.pcohptr.get_persistence()
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 :func:`compute_persistence` function to be
launched first.
:note: This function always returns the Betti numbers of a torus as infinity
filtration cubes are not removed from the complex.
"""
assert self.pcohptr != NULL, "compute_persistence() must be called before betti_numbers()"
return self.pcohptr.betti_numbers()
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 :func:`compute_persistence`
function to be launched first.
"""
assert self.pcohptr != NULL, "compute_persistence() must be called before persistent_betti_numbers()"
return self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value)
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 dimension: int.
:returns: The persistence intervals.
:rtype: numpy array of dimension 2
:note: intervals_in_dim function requires :func:`compute_persistence` function to be
launched first.
"""
assert self.pcohptr != NULL, "compute_persistence() must be called before persistence_intervals_in_dimension()"
return np.array(self.pcohptr.intervals_in_dimension(dimension))
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