From 58d923b13afb9b18a2d5b028c6575baee691d182 Mon Sep 17 00:00:00 2001 From: MathieuCarriere Date: Tue, 17 Mar 2020 12:14:49 -0400 Subject: update python doc --- src/Simplex_tree/include/gudhi/Simplex_tree.h | 8 +++---- src/python/gudhi/simplex_tree.pyx | 34 +++++++++++++++++++++++---- 2 files changed, 33 insertions(+), 9 deletions(-) (limited to 'src') diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 02f2c7e9..f661f687 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1478,8 +1478,8 @@ class Simplex_tree { * \post The coordinates of the persistence diagram points might be a little different than the * original filtration values due to the internal transformation (scaling to [-2,-1]) that is * performed on these values during the computation of extended persistence. - * @param[in] dgm Persistence diagram obtained after calling this->extend_filtration - * and this->get_persistence. + * @param[in] dgm Persistence diagram obtained after calling this->extend_filtration, + * this->initialize_filtration, and this->compute_persistent_cohomology. * @return 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. @@ -1538,14 +1538,14 @@ class Simplex_tree { int maxvert = std::numeric_limits::min(); this->minval_ = std::numeric_limits::max(); this->maxval_ = std::numeric_limits::min(); - for (auto sh : this->skeleton_simplex_range(0)) { + for (auto sh = root_.members().begin(); sh != root_.members().end(); ++sh){ double f = this->filtration(sh); this->minval_ = std::min(this->minval_, f); this->maxval_ = std::max(this->maxval_, f); maxvert = std::max(*this->simplex_vertex_range(sh).begin(), maxvert); } - assert (maxvert < std::numeric_limits::max()); + GUDHI_CHECK(maxvert < std::numeric_limits::max(), std::invalid_argument("Simplex_tree contains a vertex with the largest Vertex_handle")); maxvert += 1; Simplex_tree* st_copy = new Simplex_tree(*this); diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 733ecb97..7af44683 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -397,19 +397,43 @@ cdef class SimplexTree: return self.get_ptr().make_filtration_non_decreasing() def extend_filtration(self): - """ Extend filtration for computing extended persistence. This function only uses the filtration values at the 0-dimensional simplices, and computes the extended persistence diagram induced by the lower-star filtration computed with these values. Note that after calling this function, the filtration values are actually modified. The function :func:`compute_extended_persistence_subdiagrams()` retrieves the original values and separates the extended persistence diagram points w.r.t. their types (Ord, Rel, Ext+, Ext-) and should always be called after computing the persistent homology of the extended simplicial complex. + """ Extend filtration for computing extended persistence. This function only uses the + filtration values at the 0-dimensional simplices, and computes the extended persistence + diagram induced by the lower-star filtration computed with these values. + + .. note:: + + Note that after calling this function, the filtration + values are actually modified within the Simplex_tree. + The function :func:`compute_extended_persistence_subdiagrams()` + retrieves the original values. + + .. note:: + + 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() def compute_extended_persistence_subdiagrams(self, dgm): - """This function retrieves good values for extended persistence, and separate the diagrams into the ordinary, relative, extended+ and extended- subdiagrams. + """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()`. + + :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:: - :param dgm: Persistence diagram obtained after calling :func:`extend_filtration()` and :func:`persistence()`. - :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-. + This function should be called only if :func:`extend_filtration()`, + :func:`initialize_filtration()`, + and :func:`persistence()` have been called first! .. note:: - This function should be called only after calling :func:`extend_filtration()` and :func:`persistence()`. + The coordinates of the persistence diagram points might be a little different than the + 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) -- cgit v1.2.3