diff options
author | mathieu <mathieu.carriere3@gmail.com> | 2020-01-16 15:46:41 -0500 |
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committer | mathieu <mathieu.carriere3@gmail.com> | 2020-01-16 15:46:41 -0500 |
commit | 436a7fbe36a9de6a969afd5978c3d496773a8690 (patch) | |
tree | a753b0c4c0648bac78b8e8b9cf11f1522866bd32 /src/python/gudhi | |
parent | cabc43b34723efa7640313348b844eabe9971e38 (diff) |
added wrapper functions
Diffstat (limited to 'src/python/gudhi')
-rw-r--r-- | src/python/gudhi/cubical_complex.pyx | 29 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pxd | 1 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pyx | 28 |
3 files changed, 56 insertions, 2 deletions
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx index cbeda014..5562e8a7 100644 --- a/src/python/gudhi/cubical_complex.pyx +++ b/src/python/gudhi/cubical_complex.pyx @@ -31,6 +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_persistence_cubical_generators(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) @@ -85,7 +86,7 @@ cdef class CubicalComplex: elif ((dimensions is None) and (top_dimensional_cells is None) and (perseus_file != '')): if os.path.isfile(perseus_file): - self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file.encode('utf-8')) + self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file)) else: print("file " + perseus_file + " not found.") else: @@ -145,6 +146,32 @@ cdef class CubicalComplex: persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) return persistence_result + def persistence_generators(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 corresponding generators, i.e., the positive and negative top-dimensional cells. + :rtype: list of pairs(dimension, pair(index of positive top-dimensional cell, index of negative top-dimensional cell)) + """ + 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_persistence_cubical_generators(homology_coeff_field, min_persistence) + return persistence_result + def betti_numbers(self): """This function returns the Betti numbers of the complex. diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 1066d44b..9e52a8aa 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -48,6 +48,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>": Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * 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, vector[int]], pair[double, vector[int]]]]] get_persistence_generators(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) diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index b18627c4..8cc58f8f 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -412,6 +412,32 @@ cdef class SimplexTree: persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) return persistence_result + def persistence_generators(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 corresponding generators, i.e., the positive and negative simplices. + :rtype: list of pairs(dimension, pair(positive_simplex, negative_simplex)) + """ + if self.pcohptr != NULL: + del self.pcohptr + self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), persistence_dim_max) + cdef vector[pair[int, pair[pair[double, vector[int]], pair[double, vector[int]]]]] persistence_result + if self.pcohptr != NULL: + persistence_result = self.pcohptr.get_persistence_generators(homology_coeff_field, min_persistence) + return persistence_result + def betti_numbers(self): """This function returns the Betti numbers of the simplicial complex. @@ -508,7 +534,7 @@ cdef class SimplexTree: """ if self.pcohptr != NULL: if persistence_file != '': - self.pcohptr.write_output_diagram(persistence_file.encode('utf-8')) + self.pcohptr.write_output_diagram(str.encode(persistence_file)) else: print("persistence_file must be specified") else: |