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author | mathieu <mathieu.carriere3@gmail.com> | 2020-02-13 19:27:40 -0500 |
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committer | mathieu <mathieu.carriere3@gmail.com> | 2020-02-13 19:27:40 -0500 |
commit | fe754ca20cf942e2af186f14e5a3d24e23b6c80e (patch) | |
tree | c85794f55195075bee036b9638e32abe04b1f003 /src/python/gudhi | |
parent | 7618fa076d848bd213b444dc5974826be5528ab1 (diff) |
fix Marc's comments
Diffstat (limited to 'src/python/gudhi')
-rw-r--r-- | src/python/gudhi/cubical_complex.pyx | 49 |
1 files changed, 25 insertions, 24 deletions
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx index bd432834..8cf43539 100644 --- a/src/python/gudhi/cubical_complex.pyx +++ b/src/python/gudhi/cubical_complex.pyx @@ -31,7 +31,7 @@ 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[pair[int, pair[pair[double, int], pair[double, int]]]] get_cofaces_of_cubical_persistence_pairs(int homology_coeff_field, double min_persistence) + vector[vector[int]] cofaces_of_cubical_persistence_pairs() vector[int] betti_numbers() vector[int] persistent_betti_numbers(double from_value, double to_value) vector[pair[double,double]] intervals_in_dimension(int dimension) @@ -146,31 +146,32 @@ cdef class CubicalComplex: persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) return persistence_result - def cofaces_of_cubical_persistence_pairs(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False): - """This function returns the persistence of the simplicial complex. - - :param homology_coeff_field: The homology coefficient field. Must be a - prime number. Default value is 11. - :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. - :param persistence_dim_max: If true, the persistent homology for the - maximal dimension in the complex is computed. If false, it is - ignored. Default is false. - :type persistence_dim_max: bool - :returns: The persistence of the simplicial complex, together with the cofaces of the corresponding generators, i.e., the top-dimensional cells/cofaces of the positive and negative simplices. - :rtype: list of pairs(dimension, pair(index of positive top-dimensional cell, index of negative top-dimensional cell)) + def cofaces_of_persistence_pairs(self): + """A persistence interval is described by a pair of cells, one that creates the + feature and one that kills it. The filtration values of those 2 cells give coordinates + for a point in a persistence diagram, or a bar in a barcode. Structurally, in the + cubical complexes provided here, the filtration value of any cell is the minimum of the + filtration values of the maximal cells that contain it. Connecting persistence diagram + coordinates to the corresponding value in the input (i.e. the filtration values of + the top-dimensional cells) is useful for differentiation purposes. + + This function returns a list of pairs of top-dimensional cells corresponding to + the persistence birth and death cells of the filtration. The cells are represented by + their indices in the input list of top-dimensional cells (and not their indices in the + internal datastructure that includes non-maximal cells). Note that when two adjacent + top-dimensional cells have the same filtration value, we arbitrarily return one of the two + when calling the function on one of their common faces. + + :returns: The top-dimensional cells/cofaces of the positive and negative cells. + :rtype: list of pairs(index of positive top-dimensional cell, index of negative top-dimensional cell) """ + cdef vector[vector[int]] persistence_result if self.pcohptr != NULL: - del self.pcohptr - self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr, True) - cdef vector[pair[int, pair[pair[double, int], pair[double, int]]]] persistence_result - if self.pcohptr != NULL: - persistence_result = self.pcohptr.get_cofaces_of_cubical_persistence_pairs(homology_coeff_field, min_persistence) - return persistence_result + persistence_result = self.pcohptr.cofaces_of_cubical_persistence_pairs() + else: + print("cofaces_of_persistence_pairs function requires persistence function" + " to be launched first.") + return np.array(persistence_result) def betti_numbers(self): """This function returns the Betti numbers of the complex. |