From 61691b0081cb868645335c0b1433ddcc0bcbf9e3 Mon Sep 17 00:00:00 2001 From: MathieuCarriere Date: Thu, 19 Mar 2020 13:09:59 -0400 Subject: new fixes --- src/python/gudhi/simplex_tree.pyx | 32 +++++++++++++++++++++++++------- 1 file changed, 25 insertions(+), 7 deletions(-) (limited to 'src/python/gudhi/simplex_tree.pyx') diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 7af44683..3502000a 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -405,7 +405,7 @@ cdef class SimplexTree: Note that after calling this function, the filtration values are actually modified within the Simplex_tree. - The function :func:`compute_extended_persistence_subdiagrams()` + The function :func:`extended_persistence()` retrieves the original values. .. note:: @@ -413,21 +413,31 @@ cdef class SimplexTree: Note that this code creates an extra vertex internally, so you should make sure that the Simplex_tree does not contain a vertex with the largest Vertex_handle. """ - return self.get_ptr().extend_filtration() + return self.get_ptr().compute_extended_filtration() - def compute_extended_persistence_subdiagrams(self, dgm): + def extended_persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False): """This function retrieves good values for extended persistence, and separate the diagrams into the ordinary, relative, extended+ and extended- subdiagrams. - :param dgm: Persistence diagram obtained after calling :func:`extend_filtration()`, :func:`initialize_filtration()`, and :func:`persistence()`. - + :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: A vector of four persistence diagrams. The first one is Ordinary, the second one is Relative, the third one is Extended+ and the fourth one is Extended-. See section 2.2 in https://link.springer.com/article/10.1007/s10208-017-9370-z for a description of these subtypes. .. note:: This function should be called only if :func:`extend_filtration()`, :func:`initialize_filtration()`, - and :func:`persistence()` have been called first! + and (optionally) :func:`persistence()` have been called first! .. note:: @@ -435,7 +445,15 @@ cdef class SimplexTree: original filtration values due to the internal transformation (scaling to [-2,-1]) that is performed on these values during the computation of extended persistence. """ - return self.get_ptr().compute_extended_persistence_subdiagrams(dgm) + cdef vector[pair[int, pair[double, double]]] persistence_result + if self.pcohptr == NULL: + self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), persistence_dim_max) + if self.pcohptr != NULL: + self.pcohptr.get_persistence(homology_coeff_field, min_persistence) + if self.pcohptr != NULL: + pairs = self.pcohptr.persistence_pairs() + persistence_result = [(len(splx1)-1, [self.filtration(splx1), self.filtration(splx2)]) for [splx1, splx2] in pairs] + return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result) def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False): -- cgit v1.2.3