diff options
Diffstat (limited to 'src/python/gudhi/simplex_tree.pyx')
| -rw-r--r-- | src/python/gudhi/simplex_tree.pyx | 71 |
1 files changed, 45 insertions, 26 deletions
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 9cb24221..dfb1d985 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -69,7 +69,7 @@ cdef class SimplexTree: this simplicial complex, or +infinity if it is not in the complex. :param simplex: The N-simplex, represented by a list of vertex. - :type simplex: list of int. + :type simplex: list of int :returns: The simplicial complex filtration value. :rtype: float """ @@ -80,7 +80,7 @@ cdef class SimplexTree: given N-simplex. :param simplex: The N-simplex, represented by a list of vertex. - :type simplex: list of int. + :type simplex: list of int :param filtration: The new filtration value. :type filtration: float @@ -153,7 +153,7 @@ cdef class SimplexTree: """This function sets the dimension of the simplicial complex. :param dimension: The new dimension value. - :type dimension: int. + :type dimension: int .. note:: @@ -172,7 +172,7 @@ cdef class SimplexTree: complex or not. :param simplex: The N-simplex to find, represented by a list of vertex. - :type simplex: list of int. + :type simplex: list of int :returns: true if the simplex was found, false otherwise. :rtype: bool """ @@ -186,9 +186,9 @@ cdef class SimplexTree: :param simplex: The N-simplex to insert, represented by a list of vertex. - :type simplex: list of int. + :type simplex: list of int :param filtration: The filtration value of the simplex. - :type filtration: float. + :type filtration: float :returns: true if the simplex was not yet in the complex, false otherwise (whatever its original filtration value). :rtype: bool @@ -225,13 +225,12 @@ cdef class SimplexTree: preincrement(it) def get_skeleton(self, dimension): - """This function returns the (simplices of the) skeleton of a maximum - given dimension. + """This function returns a generator with the (simplices of the) skeleton of a maximum given dimension. :param dimension: The skeleton dimension value. - :type dimension: int. + :type dimension: int :returns: The (simplices of the) skeleton of a maximum dimension. - :rtype: list of tuples(simplex, filtration) + :rtype: generator with tuples(simplex, filtration) """ cdef Simplex_tree_skeleton_iterator it = self.get_ptr().get_skeleton_iterator_begin(dimension) cdef Simplex_tree_skeleton_iterator end = self.get_ptr().get_skeleton_iterator_end(dimension) @@ -244,7 +243,7 @@ cdef class SimplexTree: """This function returns the star of a given N-simplex. :param simplex: The N-simplex, represented by a list of vertex. - :type simplex: list of int. + :type simplex: list of int :returns: The (simplices of the) star of a simplex. :rtype: list of tuples(simplex, filtration) """ @@ -266,10 +265,10 @@ cdef class SimplexTree: given codimension. :param simplex: The N-simplex, represented by a list of vertex. - :type simplex: list of int. + :type simplex: list of int :param codimension: The codimension. If codimension = 0, all cofaces are returned (equivalent of get_star function) - :type codimension: int. + :type codimension: int :returns: The (simplices of the) cofaces of a simplex :rtype: list of tuples(simplex, filtration) """ @@ -291,7 +290,7 @@ cdef class SimplexTree: complex. :param simplex: The N-simplex, represented by a list of vertex. - :type simplex: list of int. + :type simplex: list of int .. note:: @@ -309,7 +308,7 @@ cdef class SimplexTree: """Prune above filtration value given as parameter. :param filtration: Maximum threshold value. - :type filtration: float. + :type filtration: float :returns: The filtration modification information. :rtype: bool @@ -343,7 +342,7 @@ cdef class SimplexTree: 1 when calling the method. :param max_dim: The maximal dimension. - :type max_dim: int. + :type max_dim: int """ cdef int maxdim = max_dim with nogil: @@ -384,12 +383,12 @@ cdef class SimplexTree: :param homology_coeff_field: The homology coefficient field. Must be a prime number. Default value is 11. - :type homology_coeff_field: int. + :type homology_coeff_field: int :param min_persistence: The minimum persistence value (i.e., the absolute value of the difference between the persistence diagram point coordinates) 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. + :type min_persistence: float :returns: A list of four persistence diagrams in the format described in :func:`persistence`. The first one is Ordinary, the second one is Relative, the third one is Extended+ and the fourth one is Extended-. See https://link.springer.com/article/10.1007/s10208-008-9027-z and/or section 2.2 in https://link.springer.com/article/10.1007/s10208-017-9370-z for a description of these subtypes. .. note:: @@ -416,12 +415,12 @@ cdef class SimplexTree: :param homology_coeff_field: The homology coefficient field. Must be a prime number. Default value is 11. - :type homology_coeff_field: int. + :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. Set min_persistence to -1.0 to see all values. - :type min_persistence: float. + :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. @@ -439,12 +438,12 @@ cdef class SimplexTree: :param homology_coeff_field: The homology coefficient field. Must be a prime number. Default value is 11. - :type homology_coeff_field: int. + :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. + :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. @@ -479,10 +478,10 @@ cdef class SimplexTree: :param from_value: The persistence birth limit to be added in the numbers (persistent birth <= from_value). - :type from_value: float. + :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. + :type to_value: float :returns: The persistent Betti numbers ([B0, B1, ..., Bn]). :rtype: list of int @@ -499,7 +498,7 @@ cdef class SimplexTree: complex in a specific dimension. :param dimension: The specific dimension. - :type dimension: int. + :type dimension: int :returns: The persistence intervals. :rtype: numpy array of dimension 2 @@ -528,7 +527,7 @@ cdef class SimplexTree: complex in a user given file name. :param persistence_file: Name of the file. - :type persistence_file: string. + :type persistence_file: string :note: intervals_in_dim function requires :func:`compute_persistence` @@ -582,3 +581,23 @@ cdef class SimplexTree: infinite0 = np_array(next(l)) infinites = [np_array(d).reshape(-1,2) for d in l] return (normal0, normals, infinite0, infinites) + + def collapse_edges(self, nb_iterations = 1): + """Assuming the simplex tree is a 1-skeleton graph, this method collapse edges (simplices of higher dimension + are ignored) and resets the simplex tree from the remaining edges. + A good candidate is to build a simplex tree on top of a :class:`~gudhi.RipsComplex` of dimension 1 before + collapsing edges + (cf. :download:`rips_complex_edge_collapse_example.py <../example/rips_complex_edge_collapse_example.py>`). + For implementation details, please refer to :cite:`edgecollapsesocg2020`. + + :param nb_iterations: The number of edge collapse iterations to perform. Default is 1. + :type nb_iterations: int + """ + # Backup old pointer + cdef Simplex_tree_interface_full_featured* ptr = self.get_ptr() + cdef int nb_iter = nb_iterations + with nogil: + # New pointer is a new collapsed simplex tree + self.thisptr = <intptr_t>(ptr.collapse_edges(nb_iter)) + # Delete old pointer + del ptr |