From 85eec1ba750d56b66e3739dc486c6205f49fb31e Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 3 Jul 2020 16:04:45 +0200 Subject: A proposal for simplex_tree reset_filtration (python & C++) --- src/python/gudhi/simplex_tree.pxd | 1 + src/python/gudhi/simplex_tree.pyx | 10 ++++++++++ 2 files changed, 11 insertions(+) (limited to 'src/python/gudhi') diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index e748ac40..12c2065e 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -57,6 +57,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": bool make_filtration_non_decreasing() nogil void compute_extended_filtration() nogil vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence) nogil + void reset_filtration(double filtration, int dimension) nogil # Iterators over Simplex tree pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex) nogil Simplex_tree_simplices_iterator get_simplices_iterator_begin() nogil diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 20e66d9f..41b06116 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -358,6 +358,16 @@ cdef class SimplexTree: """ return self.get_ptr().make_filtration_non_decreasing() + def reset_filtration(self, filtration, max_dim): + """This function resets filtration value until a given dimension. + + :param filtration: New threshold value. + :type filtration: float. + :param max_dim: The maximal dimension. + :type max_dim: int. + """ + self.get_ptr().reset_filtration(filtration, max_dim) + 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 -- cgit v1.2.3 From ddb2118f0af865588d7c14b88171dc04bb27c529 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 18 Aug 2020 14:38:31 +0200 Subject: reset_filtration from a dimension (instead of 'until') --- src/Simplex_tree/include/gudhi/Simplex_tree.h | 31 ++++++++++++++---------- src/Simplex_tree/test/simplex_tree_unit_test.cpp | 14 +++++++---- src/python/gudhi/simplex_tree.pyx | 17 +++++++------ src/python/test/test_simplex_tree.py | 9 ++++--- 4 files changed, 41 insertions(+), 30 deletions(-) (limited to 'src/python/gudhi') diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index adc8e801..89b4a5df 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1668,31 +1668,36 @@ class Simplex_tree { } public: - /** \brief This function resets filtration value until a given dimension. + /** \brief This function resets filtration value from a given dimension. Resets all the Simplex_tree when + * `min_dim = 0`. * @param[in] filt_value The new filtration value. - * @param[in] max_dim The maximal dimension. + * @param[in] min_dim The minimal dimension. */ - void reset_filtration(Filtration_value filt_value, int max_dim) { + void reset_filtration(Filtration_value filt_value, int min_dim) { for (auto& simplex : root_.members()) { - simplex.second.assign_filtration(filt_value); - if (has_children(&simplex) && max_dim > 0) { - rec_reset_filtration(simplex.second.children(), filt_value, (max_dim - 1)); + if (min_dim <= 0) { + simplex.second.assign_filtration(filt_value); + } + if (has_children(&simplex)) { + rec_reset_filtration(simplex.second.children(), filt_value, min_dim); } } clear_filtration(); // Drop the cache. } private: - /** \brief Recursively resets filtration value until a given dimension. + /** \brief Recursively resets filtration value from a given dimension. * @param[in] sib Siblings to be parsed. * @param[in] filt_value The new filtration value. - * @param[in] max_dim The maximal dimension. + * @param[in] min_dim The maximal dimension. */ - void rec_reset_filtration(Siblings * sib, Filtration_value filt_value, int max_dim) { - for (auto& simplex : sib->members()) { - simplex.second.assign_filtration(filt_value); - if (has_children(&simplex) && max_dim > 0) { - rec_reset_filtration(simplex.second.children(), filt_value, (max_dim - 1)); + void rec_reset_filtration(Siblings * sib, Filtration_value filt_value, int min_dim) { + for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) { + if (min_dim <= dimension(sh)) { + sh->second.assign_filtration(filt_value); + } + if (has_children(sh)) { + rec_reset_filtration(sh->second.children(), filt_value, min_dim); } } } diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index 9780f5b0..bdd41d34 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -965,21 +965,25 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_reset_filtration, typeST, list_of_tes for (auto vertex : st.simplex_vertex_range(f_simplex)) { std::clog << vertex << ","; } - std::clog << ") - filtration =" << st.filtration(f_simplex) << std::endl; + std::clog << ") - filtration = " << st.filtration(f_simplex); + std::clog << " - dimension = " << st.dimension(f_simplex) << std::endl; + // Guaranteed by construction BOOST_CHECK(st.filtration(f_simplex) >= 2.); } // dimension until 5 even if simplex tree is of dimension 3 to test the limits - for(int dimension = 0; dimension < 6; dimension ++) { + for(int dimension = 5; dimension >= 0; dimension --) { + std::clog << "### reset_filtration - dimension = " << dimension << "\n"; st.reset_filtration(0., dimension); for (auto f_simplex : st.skeleton_simplex_range(3)) { std::clog << "vertex = ("; for (auto vertex : st.simplex_vertex_range(f_simplex)) { std::clog << vertex << ","; } - std::clog << ") - filtration =" << st.filtration(f_simplex) << std::endl; - if (st.dimension(f_simplex) > dimension) - BOOST_CHECK(st.filtration(f_simplex) >= 1.); + std::clog << ") - filtration = " << st.filtration(f_simplex); + std::clog << " - dimension = " << st.dimension(f_simplex) << std::endl; + if (st.dimension(f_simplex) < dimension) + BOOST_CHECK(st.filtration(f_simplex) >= 2.); else BOOST_CHECK(st.filtration(f_simplex) == 0.); } diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index b7682693..657d55be 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -328,7 +328,7 @@ cdef class SimplexTree: return self.get_ptr().prune_above_filtration(filtration) def expansion(self, max_dim): - """Expands the Simplex_tree containing only its one skeleton + """Expands the simplex tree containing only its one skeleton until dimension max_dim. The expanded simplicial complex until dimension :math:`d` @@ -338,7 +338,7 @@ cdef class SimplexTree: The filtration value assigned to a simplex is the maximal filtration value of one of its edges. - The Simplex_tree must contain no simplex of dimension bigger than + The simplex tree must contain no simplex of dimension bigger than 1 when calling the method. :param max_dim: The maximal dimension. @@ -358,15 +358,16 @@ cdef class SimplexTree: """ return self.get_ptr().make_filtration_non_decreasing() - def reset_filtration(self, filtration, max_dim): - """This function resets filtration value until a given dimension. + def reset_filtration(self, filtration, min_dim): + """This function resets filtration value from a given dimension. + Resets all the simplex tree when `min_dim = 0`. :param filtration: New threshold value. :type filtration: float. - :param max_dim: The maximal dimension. + :param max_dim: The minimal dimension. :type max_dim: int. """ - self.get_ptr().reset_filtration(filtration, max_dim) + self.get_ptr().reset_filtration(filtration, min_dim) def extend_filtration(self): """ Extend filtration for computing extended persistence. This function only uses the @@ -376,14 +377,14 @@ cdef class SimplexTree: .. note:: Note that after calling this function, the filtration - values are actually modified within the Simplex_tree. + values are actually modified within the simplex tree. The function :func:`extended_persistence` 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 possible value (i.e., 4294967295). + the simplex tree does not contain a vertex with the largest possible value (i.e., 4294967295). """ self.get_ptr().compute_extended_filtration() diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 6f1d01cc..ac2b59c7 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -367,15 +367,16 @@ def test_reset_filtration(): assert st.insert([3, 4, 5], 3.) == True assert st.insert([0, 1, 6, 7], 4.) == True + # Guaranteed by construction for simplex in st.get_simplices(): - assert st.filtration(simplex[0]) >= 0. + assert st.filtration(simplex[0]) >= 2. # dimension until 5 even if simplex tree is of dimension 3 to test the limits - for dimension in range(0, 6): + for dimension in range(5, -1, -1): st.reset_filtration(0., dimension) for simplex in st.get_skeleton(3): print(simplex) - if len(simplex[0]) > (dimension + 1): - assert st.filtration(simplex[0]) >= 1. + if len(simplex[0]) < (dimension) + 1: + assert st.filtration(simplex[0]) >= 2. else: assert st.filtration(simplex[0]) == 0. -- cgit v1.2.3 From 12371aa8ec7693f97200c5b3df3aa20add4ad621 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 25 Aug 2020 08:43:19 +0200 Subject: Code review: min_dim = 0 as default and some doc review --- src/Simplex_tree/include/gudhi/Simplex_tree.h | 9 ++++++--- src/python/gudhi/simplex_tree.pyx | 13 ++++++++----- 2 files changed, 14 insertions(+), 8 deletions(-) (limited to 'src/python/gudhi') diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 89b4a5df..9cd51081 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1670,10 +1670,13 @@ class Simplex_tree { public: /** \brief This function resets filtration value from a given dimension. Resets all the Simplex_tree when * `min_dim = 0`. + * `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to + * make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing` + * afterwards for instance). * @param[in] filt_value The new filtration value. - * @param[in] min_dim The minimal dimension. + * @param[in] min_dim The minimal dimension. Default value is 0. */ - void reset_filtration(Filtration_value filt_value, int min_dim) { + void reset_filtration(Filtration_value filt_value, int min_dim = 0) { for (auto& simplex : root_.members()) { if (min_dim <= 0) { simplex.second.assign_filtration(filt_value); @@ -1689,7 +1692,7 @@ class Simplex_tree { /** \brief Recursively resets filtration value from a given dimension. * @param[in] sib Siblings to be parsed. * @param[in] filt_value The new filtration value. - * @param[in] min_dim The maximal dimension. + * @param[in] min_dim The minimal dimension. */ void rec_reset_filtration(Siblings * sib, Filtration_value filt_value, int min_dim) { for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) { diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 657d55be..f28990cc 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -358,14 +358,17 @@ cdef class SimplexTree: """ return self.get_ptr().make_filtration_non_decreasing() - def reset_filtration(self, filtration, min_dim): - """This function resets filtration value from a given dimension. - Resets all the simplex tree when `min_dim = 0`. + def reset_filtration(self, filtration, min_dim = 0): + """This function resets filtration value from a given dimension. Resets all the simplex tree when + `min_dim = 0`. + `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to + make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing` + afterwards for instance). :param filtration: New threshold value. :type filtration: float. - :param max_dim: The minimal dimension. - :type max_dim: int. + :param min_dim: The minimal dimension. Default value is 0. + :type min_dim: int. """ self.get_ptr().reset_filtration(filtration, min_dim) -- cgit v1.2.3 From e64dd4039e6dff35322ff01a8aa82d79c77e9c8e Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 28 Sep 2020 09:44:43 +0200 Subject: doc review: improve reset_filtration documentation --- src/Simplex_tree/include/gudhi/Simplex_tree.h | 4 ++-- src/python/gudhi/simplex_tree.pyx | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) (limited to 'src/python/gudhi') diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 70ef4c66..5afd0e23 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1668,8 +1668,8 @@ class Simplex_tree { } public: - /** \brief This function resets filtration value from a given dimension. Resets all the Simplex_tree when - * `min_dim = 0`. + /** \brief This function resets the filtration value of all the simplices of dimension at least min_dim. Resets all + * the Simplex_tree when `min_dim = 0`. * `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to * make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing` * afterwards for instance). diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index f28990cc..910711a9 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -359,8 +359,8 @@ cdef class SimplexTree: return self.get_ptr().make_filtration_non_decreasing() def reset_filtration(self, filtration, min_dim = 0): - """This function resets filtration value from a given dimension. Resets all the simplex tree when - `min_dim = 0`. + """This function resets the filtration value of all the simplices of dimension at least min_dim. Resets all the + simplex tree when `min_dim = 0`. `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing` afterwards for instance). -- cgit v1.2.3 From dda7885005c343601c6630796eb56bdcf91a559f Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Thu, 22 Oct 2020 22:23:28 +0200 Subject: Document the change It would be possible to emit the duplicate points instead of stopping, but the current implementation makes that inconvenient. --- .../include/gudhi/choose_n_farthest_points.h | 3 ++- src/python/gudhi/subsampling.pyx | 21 +++++++++++---------- 2 files changed, 13 insertions(+), 11 deletions(-) (limited to 'src/python/gudhi') diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index 38c3a76b..0e13fc5a 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -48,7 +48,8 @@ enum : std::size_t { * \tparam PointOutputIterator Output iterator whose value type is Kernel::Point_d. * \tparam DistanceOutputIterator Output iterator for distances. * \details It chooses `final_size` points from a random access range - * `input_pts` and outputs them in the output iterator `output_it`. It also + * `input_pts` (or the number of distinct points if `final_size` is larger) + * and outputs them in the output iterator `output_it`. It also * outputs the distance from each of those points to the set of previous * points in `dist_it`. * @param[in] k A kernel object. diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index f77c6f75..b11d07e5 100644 --- a/src/python/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx @@ -33,7 +33,7 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi The iteration starts with the landmark `starting point`. :param points: The input point set. - :type points: Iterable[Iterable[float]]. + :type points: Iterable[Iterable[float]] Or @@ -42,14 +42,15 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi And in both cases - :param nb_points: Number of points of the subsample. - :type nb_points: unsigned. + :param nb_points: Number of points of the subsample (the subsample may be \ + smaller if there are fewer than nb_points distinct input points) + :type nb_points: int :param starting_point: The iteration starts with the landmark `starting \ - point`,which is the index of the point to start with. If not set, this \ + point`, which is the index of the point to start with. If not set, this \ index is chosen randomly. - :type starting_point: unsigned. + :type starting_point: int :returns: The subsample point set. - :rtype: List[List[float]]. + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): @@ -76,7 +77,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): """Subsample a point set by picking random vertices. :param points: The input point set. - :type points: Iterable[Iterable[float]]. + :type points: Iterable[Iterable[float]] Or @@ -86,7 +87,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): And in both cases :param nb_points: Number of points of the subsample. - :type nb_points: unsigned. + :type nb_points: int :returns: The subsample point set. :rtype: List[List[float]] """ @@ -107,7 +108,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): between any two points is greater than or equal to min_squared_dist. :param points: The input point set. - :type points: Iterable[Iterable[float]]. + :type points: Iterable[Iterable[float]] Or @@ -118,7 +119,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): :param min_squared_dist: Minimum squared distance separating the output \ points. - :type min_squared_dist: float. + :type min_squared_dist: float :returns: The subsample point set. :rtype: List[List[float]] """ -- cgit v1.2.3