From 88a36ffad6c11279990c1c96df32b95c1f6f526c Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 3 Jul 2020 13:57:49 +0200 Subject: A fix proposal for boudaries of a simplex python version --- .../include/gudhi/Simplex_tree/Simplex_tree_iterators.h | 5 +++++ src/python/gudhi/simplex_tree.pxd | 8 ++++++++ src/python/gudhi/simplex_tree.pyx | 16 ++++++++++++++++ src/python/include/Simplex_tree_interface.h | 11 +++++++++++ src/python/test/test_simplex_tree.py | 9 +++++++++ 5 files changed, 49 insertions(+) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index 9007b6bd..9c864454 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -85,6 +85,11 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< typedef typename SimplexTree::Vertex_handle Vertex_handle; typedef typename SimplexTree::Siblings Siblings; + Simplex_tree_boundary_simplex_iterator() + : sib_(nullptr), + st_(nullptr) { + } + // any end() iterator explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st) : last_(st->null_vertex()), diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index e748ac40..a64599e7 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -36,6 +36,12 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": Simplex_tree_skeleton_iterator operator++() nogil bint operator!=(Simplex_tree_skeleton_iterator) nogil + cdef cppclass Simplex_tree_boundary_iterator "Gudhi::Simplex_tree_interface::Boundary_simplex_iterator": + Simplex_tree_boundary_iterator() nogil + Simplex_tree_simplex_handle& operator*() nogil + Simplex_tree_boundary_iterator operator++() nogil + bint operator!=(Simplex_tree_boundary_iterator) nogil + cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface": Simplex_tree() nogil @@ -65,6 +71,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end() nogil Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil + Simplex_tree_boundary_iterator get_boundary_iterator_begin(vector[int] simplex) nogil + Simplex_tree_boundary_iterator get_boundary_iterator_end(vector[int] simplex) nogil cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface>": diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 20e66d9f..da445a12 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -285,6 +285,22 @@ cdef class SimplexTree: ct.append((v, filtered_simplex.second)) return ct + def get_boundaries(self, simplex): + """This function returns a generator with the boundaries of a given N-simplex. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + :returns: The (simplices of the) boundaries of a simplex + :rtype: generator with tuples(simplex, filtration) + """ + cdef Simplex_tree_boundary_iterator it = self.get_ptr().get_boundary_iterator_begin(simplex) + cdef Simplex_tree_boundary_iterator end = self.get_ptr().get_boundary_iterator_end(simplex) + + while it != end: + yield self.get_ptr().get_simplex_and_filtration(dereference(it)) + preincrement(it) + + def remove_maximal_simplex(self, simplex): """This function removes a given maximal N-simplex from the simplicial complex. diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index 56d7c41d..c4f18eeb 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -36,6 +36,7 @@ class Simplex_tree_interface : public Simplex_tree { using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator; using Complex_simplex_iterator = typename Base::Complex_simplex_iterator; using Extended_filtration_data = typename Base::Extended_filtration_data; + using Boundary_simplex_iterator = typename Base::Boundary_simplex_iterator; public: @@ -188,6 +189,16 @@ class Simplex_tree_interface : public Simplex_tree { // this specific case works because the range is just a pair of iterators - won't work if range was a vector return Base::skeleton_simplex_range(dimension).end(); } + + Boundary_simplex_iterator get_boundary_iterator_begin(const Simplex& simplex) { + // this specific case works because the range is just a pair of iterators - won't work if range was a vector + return Base::boundary_simplex_range(Base::find(simplex)).begin(); + } + + Boundary_simplex_iterator get_boundary_iterator_end(const Simplex& simplex) { + // this specific case works because the range is just a pair of iterators - won't work if range was a vector + return Base::boundary_simplex_range(Base::find(simplex)).end(); + } }; } // namespace Gudhi diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 2137d822..7c49cb1a 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -340,3 +340,12 @@ def test_simplices_iterator(): assert st.find(simplex[0]) == True print("filtration is: ", simplex[1]) assert st.filtration(simplex[0]) == simplex[1] + +def test_boundaries_iterator(): + st = SimplexTree() + + assert st.insert([0, 1, 2, 3], filtration=1.0) == True + assert st.insert([1, 2, 3, 4], filtration=2.0) == True + + assert list(st.get_boundaries([1, 2, 3])) == [([1, 2], 1.0), ([1, 3], 1.0), ([2, 3], 1.0)] + assert list(st.get_boundaries([2, 3, 4])) == [([2, 3], 1.0), ([2, 4], 2.0), ([3, 4], 2.0)] -- cgit v1.2.3 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/Simplex_tree/include/gudhi/Simplex_tree.h | 30 +++++++++++++++ src/Simplex_tree/test/simplex_tree_unit_test.cpp | 47 ++++++++++++++++++++++++ src/python/gudhi/simplex_tree.pxd | 1 + src/python/gudhi/simplex_tree.pyx | 10 +++++ src/python/test/test_simplex_tree.py | 22 +++++++++++ 5 files changed, 110 insertions(+) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 889dbd00..adc8e801 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1667,6 +1667,36 @@ class Simplex_tree { return sh; // None of its faces has the same filtration. } + public: + /** \brief This function resets filtration value until a given dimension. + * @param[in] filt_value The new filtration value. + * @param[in] max_dim The maximal dimension. + */ + void reset_filtration(Filtration_value filt_value, int max_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)); + } + } + clear_filtration(); // Drop the cache. + } + + private: + /** \brief Recursively resets filtration value until 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. + */ + 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)); + } + } + } + private: Vertex_handle null_vertex_; /** \brief Total number of simplices in the complex, without the empty simplex.*/ diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index 9b5fa8fe..9780f5b0 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -940,3 +940,50 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(generators, typeST, list_of_tested_variants) { BOOST_CHECK(st.edge_with_same_filtration(st.find({1,5}))==st.find({1,5})); } } + +BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_reset_filtration, typeST, list_of_tested_variants) { + std::clog << "********************************************************************" << std::endl; + std::clog << "TEST RESET FILTRATION" << std::endl; + typeST st; + + st.insert_simplex_and_subfaces({2, 1, 0}, 3.); + st.insert_simplex_and_subfaces({3, 0}, 2.); + st.insert_simplex_and_subfaces({3, 4, 5}, 3.); + st.insert_simplex_and_subfaces({0, 1, 6, 7}, 4.); + + /* Inserted simplex: */ + /* 1 6 */ + /* o---o */ + /* /X\7/ */ + /* o---o---o---o */ + /* 2 0 3\X/4 */ + /* o */ + /* 5 */ + + 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; + 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 ++) { + 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.); + else + BOOST_CHECK(st.filtration(f_simplex) == 0.); + } + } + +} + 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 diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 2137d822..1ca84c10 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -340,3 +340,25 @@ def test_simplices_iterator(): assert st.find(simplex[0]) == True print("filtration is: ", simplex[1]) assert st.filtration(simplex[0]) == simplex[1] + +def test_reset_filtration(): + st = SimplexTree() + + assert st.insert([0, 1, 2], 3.) == True + assert st.insert([0, 3], 2.) == True + assert st.insert([3, 4, 5], 3.) == True + assert st.insert([0, 1, 6, 7], 4.) == True + + for simplex in st.get_simplices(): + assert st.filtration(simplex[0]) >= 0. + + # dimension until 5 even if simplex tree is of dimension 3 to test the limits + for dimension in range(0, 6): + 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. + else: + assert st.filtration(simplex[0]) == 0. + -- cgit v1.2.3 From c2aa4a3416bbdc09840217a8dcd89da7d9647513 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 28 Jul 2020 09:37:06 +0200 Subject: Remove Eigen compilation error for Alpha complex 3d --- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index f56e12d0..2c1b97a4 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -56,10 +56,6 @@ # error Alpha_complex_3d is only available for CGAL >= 4.11 #endif -#if !EIGEN_VERSION_AT_LEAST(3,1,0) -# error Alpha_complex_3d is only available for Eigen3 >= 3.1.0 installed with CGAL -#endif - namespace Gudhi { namespace alpha_complex { -- cgit v1.2.3 From 77cda62efd84ca7090d8796ca0197b03dbc22350 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> Date: Wed, 12 Aug 2020 07:28:31 +0200 Subject: Update src/python/gudhi/simplex_tree.pyx Co-authored-by: Marc Glisse --- src/python/gudhi/simplex_tree.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index da445a12..3ebae923 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -290,7 +290,7 @@ cdef class SimplexTree: :param simplex: The N-simplex, represented by a list of vertex. :type simplex: list of int. - :returns: The (simplices of the) boundaries of a simplex + :returns: The (simplices of the) boundary of a simplex :rtype: generator with tuples(simplex, filtration) """ cdef Simplex_tree_boundary_iterator it = self.get_ptr().get_boundary_iterator_begin(simplex) -- cgit v1.2.3 From 1f31e5ce995b0e7683c4eab7077317e28ee5b1b3 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 12 Aug 2020 08:02:00 +0200 Subject: code review: add a comment about Simplex_tree_boundary_simplex_iterator default ctor --- src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index 9c864454..ee64a277 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -85,6 +85,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< typedef typename SimplexTree::Vertex_handle Vertex_handle; typedef typename SimplexTree::Siblings Siblings; + // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is overwritten. Simplex_tree_boundary_simplex_iterator() : sib_(nullptr), st_(nullptr) { -- cgit v1.2.3 From 8f9c065df7f4629555ef09292c14c293891f1bdc Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 12 Aug 2020 10:03:26 +0200 Subject: code review: Add test to get boundaries from a vertex --- src/python/test/test_simplex_tree.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 7c49cb1a..036e88df 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -349,3 +349,4 @@ def test_boundaries_iterator(): assert list(st.get_boundaries([1, 2, 3])) == [([1, 2], 1.0), ([1, 3], 1.0), ([2, 3], 1.0)] assert list(st.get_boundaries([2, 3, 4])) == [([2, 3], 1.0), ([2, 4], 2.0), ([3, 4], 2.0)] + assert list(st.get_boundaries([2])) == [] -- cgit v1.2.3 From 458bc2dcf5044e1d5fde5326b2be35e526abd457 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 12 Aug 2020 13:06:03 +0200 Subject: code review: boundaries uses only once find and return a pair of iterator. Exception is raised when not found. tested --- src/python/gudhi/simplex_tree.pxd | 3 +-- src/python/gudhi/simplex_tree.pyx | 14 ++++++++------ src/python/include/Simplex_tree_interface.h | 12 +++++------- src/python/test/test_simplex_tree.py | 9 +++++++++ 4 files changed, 23 insertions(+), 15 deletions(-) diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index a64599e7..e1b03391 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -71,8 +71,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end() nogil Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil - Simplex_tree_boundary_iterator get_boundary_iterator_begin(vector[int] simplex) nogil - Simplex_tree_boundary_iterator get_boundary_iterator_end(vector[int] simplex) nogil + pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] get_boundary_iterators(vector[int] simplex) nogil except + cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface>": diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 3ebae923..bc5b43f4 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -293,12 +293,14 @@ cdef class SimplexTree: :returns: The (simplices of the) boundary of a simplex :rtype: generator with tuples(simplex, filtration) """ - cdef Simplex_tree_boundary_iterator it = self.get_ptr().get_boundary_iterator_begin(simplex) - cdef Simplex_tree_boundary_iterator end = self.get_ptr().get_boundary_iterator_end(simplex) - - while it != end: - yield self.get_ptr().get_simplex_and_filtration(dereference(it)) - preincrement(it) + cdef pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] it = self.get_ptr().get_boundary_iterators(simplex) + + try: + while it.first != it.second: + yield self.get_ptr().get_simplex_and_filtration(dereference(it.first)) + preincrement(it.first) + except RuntimeError: + print("simplex not found - cannot find boundaries") def remove_maximal_simplex(self, simplex): diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index c4f18eeb..2c695d1b 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -190,14 +190,12 @@ class Simplex_tree_interface : public Simplex_tree { return Base::skeleton_simplex_range(dimension).end(); } - Boundary_simplex_iterator get_boundary_iterator_begin(const Simplex& simplex) { + std::pair get_boundary_iterators(const Simplex& simplex) { + auto bd_sh = Base::find(simplex); + if (bd_sh == Base::null_simplex()) + throw std::runtime_error("simplex not found - cannot find boundaries"); // this specific case works because the range is just a pair of iterators - won't work if range was a vector - return Base::boundary_simplex_range(Base::find(simplex)).begin(); - } - - Boundary_simplex_iterator get_boundary_iterator_end(const Simplex& simplex) { - // this specific case works because the range is just a pair of iterators - won't work if range was a vector - return Base::boundary_simplex_range(Base::find(simplex)).end(); + return std::make_pair(Base::boundary_simplex_range(bd_sh).begin(), Base::boundary_simplex_range(bd_sh).end()); } }; diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 036e88df..828400fb 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -350,3 +350,12 @@ def test_boundaries_iterator(): assert list(st.get_boundaries([1, 2, 3])) == [([1, 2], 1.0), ([1, 3], 1.0), ([2, 3], 1.0)] assert list(st.get_boundaries([2, 3, 4])) == [([2, 3], 1.0), ([2, 4], 2.0), ([3, 4], 2.0)] assert list(st.get_boundaries([2])) == [] + + with pytest.raises(RuntimeError): + list(st.get_boundaries([])) + + with pytest.raises(RuntimeError): + list(st.get_boundaries([0, 4])) # (0, 4) does not exist + + with pytest.raises(RuntimeError): + list(st.get_boundaries([6])) # (6) does not exist -- 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(-) 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 ad7e537f37c93cba6e2b391bf68783359362afa4 Mon Sep 17 00:00:00 2001 From: yuichi-ike Date: Wed, 19 Aug 2020 13:49:27 +0900 Subject: docs modified --- src/python/doc/rips_complex_sum.inc | 22 +++++++++++----------- src/python/doc/rips_complex_user.rst | 6 +++--- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/python/doc/rips_complex_sum.inc b/src/python/doc/rips_complex_sum.inc index c123ea2a..2cb24990 100644 --- a/src/python/doc/rips_complex_sum.inc +++ b/src/python/doc/rips_complex_sum.inc @@ -1,14 +1,14 @@ .. table:: :widths: 30 40 30 - +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------+ - | .. figure:: | The Vietoris-Rips complex is a simplicial complex built as the | :Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse | - | ../../doc/Rips_complex/rips_complex_representation.png | clique-complex of a proximity graph. | | - | :figclass: align-center | | :Since: GUDHI 2.0.0 | - | | We also provide sparse approximations, to speed-up the computation | | - | | of persistent homology, and weighted versions, which are more robust | :License: MIT | - | | to outliers. | | - | | | | - +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------+ - | * :doc:`rips_complex_user` | * :doc:`rips_complex_ref` | - +----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------+ + +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------------------+ + | .. figure:: | The Vietoris-Rips complex is a simplicial complex built as the | :Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse, Yuichi Ike | + | ../../doc/Rips_complex/rips_complex_representation.png | clique-complex of a proximity graph. | | + | :figclass: align-center | | :Since: GUDHI 2.0.0 | + | | We also provide sparse approximations, to speed-up the computation | | + | | of persistent homology, and weighted versions, which are more robust | :License: MIT | + | | to outliers. | | + | | | | + +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------------------+ + | * :doc:`rips_complex_user` | * :doc:`rips_complex_ref` | + +----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst index 6048cc4e..27d218d4 100644 --- a/src/python/doc/rips_complex_user.rst +++ b/src/python/doc/rips_complex_user.rst @@ -7,9 +7,9 @@ Rips complex user manual Definition ---------- -==================================================================== ================================ ====================== -:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse :Since: GUDHI 2.0.0 :License: GPL v3 -==================================================================== ================================ ====================== +================================================================================ ================================ ====================== +:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse, Yuichi Ike :Since: GUDHI 2.0.0 :License: GPL v3 +================================================================================ ================================ ====================== +-------------------------------------------+----------------------------------------------------------------------+ | :doc:`rips_complex_user` | :doc:`rips_complex_ref` | -- cgit v1.2.3 From 6128a88a6780af29825c73af0e32100e93c2f0b5 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 19 Aug 2020 11:34:06 +0200 Subject: python code coverage on python circleci target. Fix language_level cython warning --- .circleci/config.yml | 10 ++++++---- src/python/setup.py.in | 6 +++--- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index b04efd52..f8dae062 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -57,20 +57,22 @@ jobs: cmake -DUSER_VERSION_DIR=version ..; make user_version; cd version; - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..; + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .; cd python; python3 setup.py build_ext --inplace; make sphinx; cp -R sphinx /tmp/sphinx; python3 setup.py install; python3 setup.py clean --all; - ctest -j 2 --output-on-failure; + python3 -B -m pytest test/*.py --cov-report html --cov=gudhi; + cp -R htmlcov /tmp/htmlcov; - store_artifacts: path: /tmp/sphinx + - store_artifacts: + path: /tmp/htmlcov + doxygen: docker: - image: gudhi/ci_for_gudhi:latest diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 98d058fc..3602fa42 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -32,7 +32,7 @@ runtime_library_dirs=[@GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS@] # Create ext_modules list from module list ext_modules = [] for module in cython_modules: - ext_modules.append(Extension( + extension = Extension( 'gudhi.' + module, sources = [source_dir + module + '.pyx',], language = 'c++', @@ -41,8 +41,8 @@ for module in cython_modules: libraries=libraries, library_dirs=library_dirs, include_dirs=include_dirs, - runtime_library_dirs=runtime_library_dirs, - cython_directives = {'language_level': str(sys.version_info[0])},)) + runtime_library_dirs=runtime_library_dirs,) + extension.cython_directives = {'language_level': str(sys.version_info[0])} ext_modules = cythonize(ext_modules) -- cgit v1.2.3 From bcad92a18c40b9926b3b25688ab5435c301990df Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 19 Aug 2020 11:40:40 +0200 Subject: need to append --- src/python/setup.py.in | 1 + 1 file changed, 1 insertion(+) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 3602fa42..f211f5d2 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -43,6 +43,7 @@ for module in cython_modules: include_dirs=include_dirs, runtime_library_dirs=runtime_library_dirs,) extension.cython_directives = {'language_level': str(sys.version_info[0])} + ext_modules.append(extension) ext_modules = cythonize(ext_modules) -- cgit v1.2.3 From 52cb44a02ad8ce9884db63724ea0a5f1e35c6172 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 19 Aug 2020 12:00:27 +0200 Subject: Try to setup.py clean failure --- .circleci/config.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index f8dae062..77fad2ee 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -57,14 +57,16 @@ jobs: cmake -DUSER_VERSION_DIR=version ..; make user_version; cd version; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .; + mkdir build; + cd build; + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..; cd python; python3 setup.py build_ext --inplace; make sphinx; cp -R sphinx /tmp/sphinx; python3 setup.py install; python3 setup.py clean --all; - python3 -B -m pytest test/*.py --cov-report html --cov=gudhi; + python3 -B -m pytest ../../python/test/*.py --cov-report html --cov=gudhi; cp -R htmlcov /tmp/htmlcov; - store_artifacts: -- cgit v1.2.3 From 4a572af654afc22e2f5c26766f611b1918313509 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 20 Aug 2020 08:15:19 +0200 Subject: Roll back - why cannot clean ? --- .circleci/config.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 77fad2ee..eca9f91e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -66,15 +66,11 @@ jobs: cp -R sphinx /tmp/sphinx; python3 setup.py install; python3 setup.py clean --all; - python3 -B -m pytest ../../python/test/*.py --cov-report html --cov=gudhi; - cp -R htmlcov /tmp/htmlcov; + ctest -j 2 --output-on-failure; - store_artifacts: path: /tmp/sphinx - - store_artifacts: - path: /tmp/htmlcov - doxygen: docker: - image: gudhi/ci_for_gudhi:latest -- cgit v1.2.3 From 37786db094d0251bf070215e89e4446384dbe871 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 20 Aug 2020 09:35:31 +0200 Subject: Let's clean fail --- .circleci/config.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index eca9f91e..129fdc23 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -57,19 +57,19 @@ jobs: cmake -DUSER_VERSION_DIR=version ..; make user_version; cd version; - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..; + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .; cd python; python3 setup.py build_ext --inplace; make sphinx; cp -R sphinx /tmp/sphinx; python3 setup.py install; - python3 setup.py clean --all; - ctest -j 2 --output-on-failure; - + python3 setup.py clean --all || true; + python3 -B -m pytest test/*.py --cov-report html --cov=gudhi; + cp -R htmlcov /tmp/htmlcov; - store_artifacts: path: /tmp/sphinx + - store_artifacts: + path: /tmp/htmlcov doxygen: docker: -- cgit v1.2.3 From 151350f85c2799bcb2fde04c6746db7ab7e1ac95 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 20 Aug 2020 10:28:48 +0200 Subject: Add some debug traces and install pytest-cov for code coverage --- .circleci/config.yml | 1 + .github/test-requirements.txt | 1 + 2 files changed, 2 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 129fdc23..167cb4db 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -64,6 +64,7 @@ jobs: cp -R sphinx /tmp/sphinx; python3 setup.py install; python3 setup.py clean --all || true; + python3 -m pip list python3 -B -m pytest test/*.py --cov-report html --cov=gudhi; cp -R htmlcov /tmp/htmlcov; - store_artifacts: diff --git a/.github/test-requirements.txt b/.github/test-requirements.txt index 98f1007e..7d69c0b9 100644 --- a/.github/test-requirements.txt +++ b/.github/test-requirements.txt @@ -1,4 +1,5 @@ pytest +pytest-cov sphinx sphinxcontrib-bibtex sphinx-paramlinks -- cgit v1.2.3 From 129e85610cfd5a1e3db7f7d656e99915b96a3be5 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 20 Aug 2020 14:17:31 +0200 Subject: Some cleanup. CircleCI docker image build requires update --- .circleci/config.yml | 76 ++++++++++++++++++++++--------------------- Dockerfile_for_circleci_image | 3 ++ 2 files changed, 42 insertions(+), 37 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 167cb4db..285a66a5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -8,11 +8,11 @@ jobs: - run: name: Build and test examples command: | - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..; - make all; - ctest --output-on-failure; + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF .. + make all + ctest --output-on-failure tests: docker: @@ -22,11 +22,11 @@ jobs: - run: name: Build and test unitary tests command: | - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..; - make all; - ctest --output-on-failure; + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF .. + make all + ctest --output-on-failure utils: docker: @@ -36,11 +36,11 @@ jobs: - run: name: Build and test utilities command: | - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF ..; - make all; - ctest --output-on-failure; + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF .. + make all + ctest --output-on-failure python: docker: @@ -52,25 +52,26 @@ jobs: command: | git submodule init git submodule update - mkdir build; - cd build; - cmake -DUSER_VERSION_DIR=version ..; - make user_version; - cd version; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .; - cd python; - python3 setup.py build_ext --inplace; - make sphinx; - cp -R sphinx /tmp/sphinx; - python3 setup.py install; - python3 setup.py clean --all || true; - python3 -m pip list - python3 -B -m pytest test/*.py --cov-report html --cov=gudhi; - cp -R htmlcov /tmp/htmlcov; + mkdir build + cd build + cmake -DUSER_VERSION_DIR=version .. + make user_version + cd version + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 . + cd python + python3 setup.py build_ext --inplace + make sphinx + cp -R sphinx /tmp/sphinx + python3 setup.py install + python3 setup.py clean --all + python3 -B -m pytest test/*.py --cov-report html --cov=gudhi + cp -R htmlcov /tmp/htmlcov - store_artifacts: path: /tmp/sphinx + destination: sphinx - store_artifacts: path: /tmp/htmlcov + destination: htmlcov doxygen: docker: @@ -82,16 +83,17 @@ jobs: command: | git submodule init git submodule update - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version ..; - make doxygen 2>&1 | tee dox.log; - grep warning dox.log; - cp dox.log version/doc/html/; - cp -R version/doc/html /tmp/doxygen; + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version .. + make doxygen 2>&1 | tee dox.log + grep warning dox.log + cp dox.log version/doc/html/ + cp -R version/doc/html /tmp/doxygen - store_artifacts: path: /tmp/doxygen + destination: doxygen workflows: version: 2 diff --git a/Dockerfile_for_circleci_image b/Dockerfile_for_circleci_image index 464097e7..87f57071 100644 --- a/Dockerfile_for_circleci_image +++ b/Dockerfile_for_circleci_image @@ -23,6 +23,9 @@ ENV LANG en_US.UTF-8 ENV LANGUAGE en_US:en ENV LC_ALL en_US.UTF-8 +# Update again +RUN apt-get update + # Required for Gudhi compilation RUN apt-get install -y make \ git \ -- cgit v1.2.3 From 3845d669233afda0cb50270e3204c87d2814626f Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 21 Aug 2020 08:11:45 +0200 Subject: Add -DCMAKE_BUILD_TYPE=Release on installation doc --- src/common/doc/installation.h | 10 +++++----- src/python/doc/installation.rst | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index ce2c5448..6af645e2 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -14,13 +14,13 @@ \verbatim cd /path-to-gudhi/ mkdir build cd build/ -cmake .. +cmake -DCMAKE_BUILD_TYPE=Release .. make \endverbatim * By default, examples are disabled. You can activate their compilation with * ccmake (on Linux and Mac OSX), * cmake-gui (on Windows) or by modifying the * cmake command as follows : -\verbatim cmake -DWITH_GUDHI_EXAMPLE=ON .. +\verbatim cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON .. make \endverbatim * A list of utilities and examples is available here. * @@ -66,9 +66,9 @@ make doxygen * Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require CGAL, a C++ library that provides * easy access to efficient and reliable geometric algorithms. * - * \note There is no need to install CGAL, you can just cmake . && make CGAL (or even - * cmake -DCGAL_HEADER_ONLY=ON .), thereafter you will be able to compile - * GUDHI by calling cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make + * \note There is no need to install CGAL, you can just cmake -DCMAKE_BUILD_TYPE=Release . && make CGAL + * (or even cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_HEADER_ONLY=ON .), thereafter you will be able to + * compile GUDHI by calling cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make * * The procedure to install this library according to * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 78e1af73..4cc31d5c 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -65,7 +65,7 @@ one can build the GUDHI Python module, by running the following commands in a te cd /path-to-gudhi/ mkdir build cd build/ - cmake .. + cmake -DCMAKE_BUILD_TYPE=Release .. cd python make -- cgit v1.2.3 From 34c3812e5c70799a184cec315e7ee9d71c7ad5b7 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 21 Aug 2020 09:56:44 +0200 Subject: Virtual functions need signatures that exactly match --- .../Bitmap_cubical_complex_periodic_boundary_conditions_base.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h index 18901469..6a18f0eb 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h @@ -83,7 +83,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * The boundary elements are guaranteed to be returned so that the * incidence coefficients are alternating. */ - virtual std::vector get_boundary_of_a_cell(std::size_t cell) const; + virtual inline std::vector get_boundary_of_a_cell(std::size_t cell) const; /** * A version of a function that return coboundary of a given cell for an object of @@ -93,7 +93,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * To compute incidence between cells use compute_incidence_between_cells * procedure */ - virtual std::vector get_coboundary_of_a_cell(std::size_t cell) const; + virtual inline std::vector get_coboundary_of_a_cell(std::size_t cell) const; /** * This procedure compute incidence numbers between cubes. For a cube \f$A\f$ of @@ -114,7 +114,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * @exception std::logic_error In case when the cube \f$B\f$ is not n-1 * dimensional face of a cube \f$A\f$. **/ - virtual int compute_incidence_between_cells(std::size_t coface, std::size_t face) { + virtual int compute_incidence_between_cells(std::size_t coface, std::size_t face) const { // first get the counters for coface and face: std::vector coface_counter = this->compute_counter_for_given_cell(coface); std::vector face_counter = this->compute_counter_for_given_cell(face); -- cgit v1.2.3 From e8cfcc7017f9002a229996232fdb2d03a41d7ea7 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 21 Aug 2020 15:40:17 +0200 Subject: Fix compilation issues when cgal but no eigen --- src/Alpha_complex/example/CMakeLists.txt | 8 ++- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 2 - src/Alpha_complex/test/CMakeLists.txt | 6 +- src/Alpha_complex/utilities/CMakeLists.txt | 4 +- src/Collapse/example/CMakeLists.txt | 41 ++++++++------ .../include/gudhi/Flag_complex_edge_collapser.h | 6 ++ src/Collapse/test/CMakeLists.txt | 16 ++++-- src/Collapse/utilities/CMakeLists.txt | 66 ++++++++++++---------- 8 files changed, 87 insertions(+), 62 deletions(-) diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 2eecd50c..6e231773 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -25,7 +25,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Alpha_complex_example_fast_from_off_32 COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt") -if (DIFF_PATH) + if (DIFF_PATH) # Do not forget to copy test results files in current binary dir file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) @@ -43,8 +43,10 @@ if (DIFF_PATH) add_test(Alpha_complex_example_fast_from_off_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) set_tests_properties(Alpha_complex_example_fast_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_32) -endif() + endif() + endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${CGAL_LIBRARY}) if (TBB_FOUND) @@ -61,4 +63,4 @@ endif() add_test(NAME Alpha_complex_example_3d_from_points COMMAND $) -endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +endif(NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 2c1b97a4..622b10ee 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -38,8 +38,6 @@ #include #include // for CGAL_VERSION_NR -#include // for EIGEN_VERSION_AT_LEAST - #include #include diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index fe4b23e4..f38bd096 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -18,6 +18,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) gudhi_add_boost_test(Alpha_complex_test_unit) gudhi_add_boost_test(Delaunay_complex_test_unit) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + +if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + add_executable ( Alpha_complex_3d_test_unit Alpha_complex_3d_unit_test.cpp ) target_link_libraries(Alpha_complex_3d_test_unit ${CGAL_LIBRARY}) add_executable ( Weighted_alpha_complex_3d_test_unit Weighted_alpha_complex_3d_unit_test.cpp ) @@ -38,4 +42,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) gudhi_add_boost_test(Periodic_alpha_complex_3d_test_unit) gudhi_add_boost_test(Weighted_periodic_alpha_complex_3d_test_unit) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 2ffbdde0..f0ddfc2c 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -27,7 +27,9 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) endif() install(TARGETS alpha_complex_persistence DESTINATION bin) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options) if (TBB_FOUND) @@ -75,4 +77,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) install(TARGETS alpha_complex_3d_persistence DESTINATION bin) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Collapse/example/CMakeLists.txt b/src/Collapse/example/CMakeLists.txt index ba0e75e3..4456a844 100644 --- a/src/Collapse/example/CMakeLists.txt +++ b/src/Collapse/example/CMakeLists.txt @@ -1,23 +1,28 @@ project(Edge_collapse_examples) -# Point cloud -add_executable ( Edge_collapse_example_basic edge_collapse_basic_example.cpp ) -if (TBB_FOUND) - target_link_libraries(Edge_collapse_example_basic ${TBB_LIBRARIES}) -endif() +if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) -add_test(NAME Edge_collapse_example_basic COMMAND $) + # Point cloud + add_executable ( Edge_collapse_example_basic edge_collapse_basic_example.cpp ) + + if (TBB_FOUND) + target_link_libraries(Edge_collapse_example_basic ${TBB_LIBRARIES}) + endif() + + add_test(NAME Edge_collapse_example_basic COMMAND $) + + # Point cloud + add_executable ( Edge_collapse_conserve_persistence edge_collapse_conserve_persistence.cpp ) + + if (TBB_FOUND) + target_link_libraries(Edge_collapse_conserve_persistence ${TBB_LIBRARIES}) + endif() + + add_test(NAME Edge_collapse_conserve_persistence_1 COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "0.2") + + add_test(NAME Edge_collapse_conserve_persistence_2 COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "1.8") -# Point cloud -add_executable ( Edge_collapse_conserve_persistence edge_collapse_conserve_persistence.cpp ) - -if (TBB_FOUND) - target_link_libraries(Edge_collapse_conserve_persistence ${TBB_LIBRARIES}) -endif() - -add_test(NAME Edge_collapse_conserve_persistence_1 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "0.2") - -add_test(NAME Edge_collapse_conserve_persistence_2 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "1.8") +endif() \ No newline at end of file diff --git a/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h b/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h index b6b7f7c1..d3aead70 100644 --- a/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h +++ b/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h @@ -18,6 +18,7 @@ #include #include +#include // for EIGEN_VERSION_AT_LEAST #ifdef GUDHI_USE_TBB #include @@ -34,6 +35,11 @@ #include // for std::inserter #include // for std::decay +// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10 +#if !EIGEN_VERSION_AT_LEAST(3,1,0) +# error Alpha_complex is only available for Eigen3 >= 3.1.0 installed with CGAL +#endif + namespace Gudhi { namespace collapse { diff --git a/src/Collapse/test/CMakeLists.txt b/src/Collapse/test/CMakeLists.txt index c7eafb46..c04199e2 100644 --- a/src/Collapse/test/CMakeLists.txt +++ b/src/Collapse/test/CMakeLists.txt @@ -1,9 +1,13 @@ project(Collapse_tests) -include(GUDHI_boost_test) +if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) -add_executable ( Collapse_test_unit collapse_unit_test.cpp ) -if (TBB_FOUND) - target_link_libraries(Collapse_test_unit ${TBB_LIBRARIES}) -endif() -gudhi_add_boost_test(Collapse_test_unit) + include(GUDHI_boost_test) + + add_executable ( Collapse_test_unit collapse_unit_test.cpp ) + if (TBB_FOUND) + target_link_libraries(Collapse_test_unit ${TBB_LIBRARIES}) + endif() + gudhi_add_boost_test(Collapse_test_unit) + +endif() \ No newline at end of file diff --git a/src/Collapse/utilities/CMakeLists.txt b/src/Collapse/utilities/CMakeLists.txt index c742144b..97fef649 100644 --- a/src/Collapse/utilities/CMakeLists.txt +++ b/src/Collapse/utilities/CMakeLists.txt @@ -1,33 +1,37 @@ project(Collapse_utilities) -# From a point cloud -add_executable ( point_cloud_edge_collapse_rips_persistence point_cloud_edge_collapse_rips_persistence.cpp ) -target_link_libraries(point_cloud_edge_collapse_rips_persistence Boost::program_options) - -if (TBB_FOUND) - target_link_libraries(point_cloud_edge_collapse_rips_persistence ${TBB_LIBRARIES}) -endif() -add_test(NAME Edge_collapse_utilities_point_cloud_rips_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "off_results.pers") - -install(TARGETS point_cloud_edge_collapse_rips_persistence DESTINATION bin) - -# From a distance matrix -add_executable ( distance_matrix_edge_collapse_rips_persistence distance_matrix_edge_collapse_rips_persistence.cpp ) -target_link_libraries(distance_matrix_edge_collapse_rips_persistence Boost::program_options) - -if (TBB_FOUND) - target_link_libraries(distance_matrix_edge_collapse_rips_persistence ${TBB_LIBRARIES}) -endif() -add_test(NAME Edge_collapse_utilities_distance_matrix_rips_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/distance_matrix/tore3D_1307_distance_matrix.csv" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "csv_results.pers") - -install(TARGETS distance_matrix_edge_collapse_rips_persistence DESTINATION bin) - -if (DIFF_PATH) - add_test(Edge_collapse_utilities_diff_persistence ${DIFF_PATH} - "off_results.pers" "csv_results.pers") - set_tests_properties(Edge_collapse_utilities_diff_persistence PROPERTIES DEPENDS - "Edge_collapse_utilities_point_cloud_rips_persistence;Edge_collapse_utilities_distance_matrix_rips_persistence") - -endif() +if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) + + # From a point cloud + add_executable ( point_cloud_edge_collapse_rips_persistence point_cloud_edge_collapse_rips_persistence.cpp ) + target_link_libraries(point_cloud_edge_collapse_rips_persistence Boost::program_options) + + if (TBB_FOUND) + target_link_libraries(point_cloud_edge_collapse_rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Edge_collapse_utilities_point_cloud_rips_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "off_results.pers") + + install(TARGETS point_cloud_edge_collapse_rips_persistence DESTINATION bin) + + # From a distance matrix + add_executable ( distance_matrix_edge_collapse_rips_persistence distance_matrix_edge_collapse_rips_persistence.cpp ) + target_link_libraries(distance_matrix_edge_collapse_rips_persistence Boost::program_options) + + if (TBB_FOUND) + target_link_libraries(distance_matrix_edge_collapse_rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Edge_collapse_utilities_distance_matrix_rips_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/distance_matrix/tore3D_1307_distance_matrix.csv" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "csv_results.pers") + + install(TARGETS distance_matrix_edge_collapse_rips_persistence DESTINATION bin) + + if (DIFF_PATH) + add_test(Edge_collapse_utilities_diff_persistence ${DIFF_PATH} + "off_results.pers" "csv_results.pers") + set_tests_properties(Edge_collapse_utilities_diff_persistence PROPERTIES DEPENDS + "Edge_collapse_utilities_point_cloud_rips_persistence;Edge_collapse_utilities_distance_matrix_rips_persistence") + + endif() + +endif() \ No newline at end of file -- cgit v1.2.3 From d9ae2cb822631d68e4ef1cec7eed0124080c0020 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 24 Aug 2020 09:17:23 +0200 Subject: code review: call boundary_simplex_range only once --- src/python/include/Simplex_tree_interface.h | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index ab3f13f1..baff3850 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -226,7 +226,8 @@ class Simplex_tree_interface : public Simplex_tree { if (bd_sh == Base::null_simplex()) throw std::runtime_error("simplex not found - cannot find boundaries"); // this specific case works because the range is just a pair of iterators - won't work if range was a vector - return std::make_pair(Base::boundary_simplex_range(bd_sh).begin(), Base::boundary_simplex_range(bd_sh).end()); + auto boundary_srange = Base::boundary_simplex_range(bd_sh); + return std::make_pair(boundary_srange.begin(), boundary_srange.end()); } }; -- cgit v1.2.3 From f424715caab7609085cf155abd98c88674ec329d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 24 Aug 2020 09:20:02 +0200 Subject: code review: really bad copy/paste... --- src/Collapse/include/gudhi/Flag_complex_edge_collapser.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h b/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h index d3aead70..713c6608 100644 --- a/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h +++ b/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h @@ -37,7 +37,7 @@ // Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10 #if !EIGEN_VERSION_AT_LEAST(3,1,0) -# error Alpha_complex is only available for Eigen3 >= 3.1.0 installed with CGAL +# error Edge Collapse is only available for Eigen3 >= 3.1.0 #endif namespace Gudhi { -- cgit v1.2.3 From 023c4cc8a4fc167a03f9c87f066c80f722c0e520 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 24 Aug 2020 10:12:01 +0200 Subject: code review: override and remove inline --- .../Bitmap_cubical_complex_periodic_boundary_conditions_base.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h index 6a18f0eb..8ac7ae23 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h @@ -83,7 +83,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * The boundary elements are guaranteed to be returned so that the * incidence coefficients are alternating. */ - virtual inline std::vector get_boundary_of_a_cell(std::size_t cell) const; + virtual std::vector get_boundary_of_a_cell(std::size_t cell) const override; /** * A version of a function that return coboundary of a given cell for an object of @@ -93,7 +93,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * To compute incidence between cells use compute_incidence_between_cells * procedure */ - virtual inline std::vector get_coboundary_of_a_cell(std::size_t cell) const; + virtual std::vector get_coboundary_of_a_cell(std::size_t cell) const override; /** * This procedure compute incidence numbers between cubes. For a cube \f$A\f$ of @@ -114,7 +114,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * @exception std::logic_error In case when the cube \f$B\f$ is not n-1 * dimensional face of a cube \f$A\f$. **/ - virtual int compute_incidence_between_cells(std::size_t coface, std::size_t face) const { + virtual int compute_incidence_between_cells(std::size_t coface, std::size_t face) const override { // first get the counters for coface and face: std::vector coface_counter = this->compute_counter_for_given_cell(coface); std::vector face_counter = this->compute_counter_for_given_cell(face); -- 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(-) 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 723252b311a7989ef1d4271b3a812ec7d0be05f2 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 25 Aug 2020 12:50:22 +0200 Subject: Code review: use minimal depth recursively instead of computing dimension on each loop --- src/Simplex_tree/include/gudhi/Simplex_tree.h | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 9cd51081..70ef4c66 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1682,25 +1682,25 @@ class Simplex_tree { simplex.second.assign_filtration(filt_value); } if (has_children(&simplex)) { - rec_reset_filtration(simplex.second.children(), filt_value, min_dim); + rec_reset_filtration(simplex.second.children(), filt_value, min_dim - 1); } } clear_filtration(); // Drop the cache. } private: - /** \brief Recursively resets filtration value from a given dimension. + /** \brief Recursively resets filtration value when minimal depth <= 0. * @param[in] sib Siblings to be parsed. * @param[in] filt_value The new filtration value. - * @param[in] min_dim The minimal dimension. + * @param[in] min_depth The minimal depth. */ - void rec_reset_filtration(Siblings * sib, Filtration_value filt_value, int min_dim) { + void rec_reset_filtration(Siblings * sib, Filtration_value filt_value, int min_depth) { for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) { - if (min_dim <= dimension(sh)) { + if (min_depth <= 0) { sh->second.assign_filtration(filt_value); } if (has_children(sh)) { - rec_reset_filtration(sh->second.children(), filt_value, min_dim); + rec_reset_filtration(sh->second.children(), filt_value, min_depth - 1); } } } -- cgit v1.2.3 From 625ff957479c8a37b4ae02bba29dfffc0d3f1a84 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 28 Aug 2020 14:38:28 +0200 Subject: code review: Rollback as these changes does not help --- src/python/setup.py.in | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index f211f5d2..d2708177 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -32,7 +32,7 @@ runtime_library_dirs=[@GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS@] # Create ext_modules list from module list ext_modules = [] for module in cython_modules: - extension = Extension( + ext_modules.append(Extension( 'gudhi.' + module, sources = [source_dir + module + '.pyx',], language = 'c++', @@ -41,9 +41,8 @@ for module in cython_modules: libraries=libraries, library_dirs=library_dirs, include_dirs=include_dirs, - runtime_library_dirs=runtime_library_dirs,) - extension.cython_directives = {'language_level': str(sys.version_info[0])} - ext_modules.append(extension) + runtime_library_dirs=runtime_library_dirs, + cython_directives = {'language_level': str(sys.version_info[0])},)) ext_modules = cythonize(ext_modules) -- cgit v1.2.3 From 4e794277bfa2158ecaeb7e9db303b92ec84a2f3c Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 28 Aug 2020 14:40:22 +0200 Subject: bad identation --- src/python/setup.py.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index d2708177..98d058fc 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -42,7 +42,7 @@ for module in cython_modules: library_dirs=library_dirs, include_dirs=include_dirs, runtime_library_dirs=runtime_library_dirs, - cython_directives = {'language_level': str(sys.version_info[0])},)) + cython_directives = {'language_level': str(sys.version_info[0])},)) ext_modules = cythonize(ext_modules) -- cgit v1.2.3 From db938dbd74460e7a0fd705be8628984052f71dc0 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 4 Sep 2020 17:23:16 +0200 Subject: Alpha_kernel_d, its tests and Alpha complex to use it --- src/Alpha_complex/example/CMakeLists.txt | 3 + .../example/Weighted_alpha_complex_from_points.cpp | 54 ++++++++ src/Alpha_complex/include/gudhi/Alpha_complex.h | 106 ++++++++-------- .../include/gudhi/Alpha_complex/Alpha_kernel_d.h | 137 +++++++++++++++++++++ .../test/Alpha_kernel_d_unit_test.cpp | 132 ++++++++++++++++++++ src/Alpha_complex/test/CMakeLists.txt | 4 + 6 files changed, 387 insertions(+), 49 deletions(-) create mode 100644 src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp create mode 100644 src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h create mode 100644 src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 2eecd50c..c9b937ed 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -7,10 +7,13 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) add_executable ( Alpha_complex_example_fast_from_off Fast_alpha_complex_from_off.cpp ) target_link_libraries(Alpha_complex_example_fast_from_off ${CGAL_LIBRARY}) + add_executable ( Weighted_alpha_complex_example_from_points Weighted_alpha_complex_from_points.cpp ) + target_link_libraries(Weighted_alpha_complex_example_from_points ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) target_link_libraries(Alpha_complex_example_fast_from_off ${TBB_LIBRARIES}) + target_link_libraries(Weighted_alpha_complex_example_from_points ${TBB_LIBRARIES}) endif() add_test(NAME Alpha_complex_example_from_points COMMAND $) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp new file mode 100644 index 00000000..19a04282 --- /dev/null +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -0,0 +1,54 @@ +#include +// to construct a simplex_tree from alpha complex +#include + +#include + +#include +#include + +// Explicit dimension 2 Epeck_d kernel +using Kernel = CGAL::Epeck_d< CGAL::Dimension_tag<2> >; +using Bare_point = Kernel::Point_d; +using Weighted_point = Kernel::Weighted_point_d; +using Vector_of_points = std::vector; + +int main() { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points points; + points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 1.)); + points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 1.)); + points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 1.)); + points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 1.)); + points.push_back(Weighted_point(Bare_point(0.0, 14.0), 1.)); + points.push_back(Weighted_point(Bare_point(2.0, 19.0), 1.)); + points.push_back(Weighted_point(Bare_point(9.0, 17.0), 1.)); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Gudhi::alpha_complex::Alpha_complex alpha_complex_from_weighted_points(points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_weighted_points.create_complex(simplex)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::clog << "Weighted alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::clog << std::endl; + } + } + return 0; +} diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index ba91998d..8e9fe773 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -12,6 +12,7 @@ #ifndef ALPHA_COMPLEX_H_ #define ALPHA_COMPLEX_H_ +#include #include // to construct Alpha_complex from a OFF file of points #include @@ -20,6 +21,7 @@ #include // isnan, fmax #include +#include // aka. Weighted Delaunay triangulation #include // For EXACT or SAFE version #include // For FAST version #include @@ -91,49 +93,55 @@ template struct Is_Epeck_D> { static const bool val * guarantee that the output is a valid filtration (faces have a filtration value no larger than their cofaces). * - For performances reasons, it is advised to use `Alpha_complex` with \ref cgal ≥ 5.0.0. */ -template> +template, bool Weighted = false> class Alpha_complex { public: + /** \brief Geometric traits class that provides the geometric types and predicates needed by the triangulations.*/ + using Geom_traits = typename std::conditional, + Kernel>::type; // Add an int in TDS to save point index in the structure - typedef CGAL::Triangulation_data_structure, - CGAL::Triangulation_full_cell > TDS; - /** \brief A Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ - typedef CGAL::Delaunay_triangulation Delaunay_triangulation; + using TDS = CGAL::Triangulation_data_structure, + CGAL::Triangulation_full_cell >; + /** \brief A (Weighted or not) Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ + using Triangulation = typename std::conditional, + CGAL::Delaunay_triangulation>::type; + + using A_kernel_d = Alpha_kernel_d; + + // Numeric type of coordinates in the kernel + using FT = typename A_kernel_d::FT; + + /** \brief If Weighted, the weighted point is cached (point + weight [= squared radius]), + * else a pair of point and squared radius is cached. + */ + using Sphere = typename A_kernel_d::Sphere; /** \brief A point in Euclidean space.*/ - typedef typename Kernel::Point_d Point_d; - /** \brief Geometric traits class that provides the geometric types and predicates needed by Delaunay - * triangulations.*/ - typedef Kernel Geom_traits; + using Point_d = typename std::conditional::type; private: - typedef typename Kernel::Compute_squared_radius_d Squared_Radius; - typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel; - typedef typename Kernel::Point_dimension_d Point_Dimension; - // Vertex_iterator type from CGAL. - typedef typename Delaunay_triangulation::Vertex_iterator CGAL_vertex_iterator; + using CGAL_vertex_iterator = typename Triangulation::Vertex_iterator; // size_type type from CGAL. - typedef typename Delaunay_triangulation::size_type size_type; + using size_type = typename Triangulation::size_type; // Structure to switch from simplex tree vertex handle to CGAL vertex iterator. - typedef typename std::vector< CGAL_vertex_iterator > Vector_vertex_iterator; - - // Numeric type of coordinates in the kernel - typedef typename Kernel::FT FT; + using Vector_vertex_iterator = typename std::vector< CGAL_vertex_iterator >; private: /** \brief Vertex iterator vector to switch from simplex tree vertex handle to CGAL vertex iterator. * Vertex handles are inserted sequentially, starting at 0.*/ Vector_vertex_iterator vertex_handle_to_iterator_; /** \brief Pointer on the CGAL Delaunay triangulation.*/ - Delaunay_triangulation* triangulation_; + Triangulation* triangulation_; /** \brief Kernel for triangulation_ functions access.*/ - Kernel kernel_; + A_kernel_d kernel_; + /** \brief Cache for geometric constructions: circumcenter and squared radius of a simplex.*/ - std::vector> cache_, old_cache_; + std::vector cache_, old_cache_; public: /** \brief Alpha_complex constructor from an OFF file name. @@ -160,10 +168,10 @@ class Alpha_complex { * * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. * - * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d + * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d or Kernel::Weighted_point_d. * * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a Kernel::Point_d. + * std::end return input iterators on a Kernel::Point_d or Kernel::Weighted_point_d. */ template Alpha_complex(const InputPointRange& points) @@ -206,11 +214,8 @@ class Alpha_complex { auto last = std::end(points); if (first != last) { - // point_dimension function initialization - Point_Dimension point_dimension = kernel_.point_dimension_d_object(); - - // Delaunay triangulation is point dimension. - triangulation_ = new Delaunay_triangulation(point_dimension(*first)); + // Delaunay triangulation init with point dimension. + triangulation_ = new Triangulation(kernel_.get_dimension(*first)); std::vector point_cloud(first, last); @@ -218,18 +223,22 @@ class Alpha_complex { std::vector indices(boost::counting_iterator(0), boost::counting_iterator(point_cloud.size())); - typedef boost::iterator_property_map::iterator, - CGAL::Identity_property_map> Point_property_map; - typedef CGAL::Spatial_sort_traits_adapter_d Search_traits_d; + using Point_property_map = boost::iterator_property_map::iterator, + CGAL::Identity_property_map>; + using Search_traits_d = CGAL::Spatial_sort_traits_adapter_d; CGAL::spatial_sort(indices.begin(), indices.end(), Search_traits_d(std::begin(point_cloud))); - typename Delaunay_triangulation::Full_cell_handle hint; + typename Triangulation::Full_cell_handle hint; for (auto index : indices) { - typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(point_cloud[index], hint); - // Save index value as data to retrieve it after insertion - pos->data() = index; - hint = pos->full_cell(); + typename Triangulation::Vertex_handle pos = triangulation_->insert(point_cloud[index], hint); + if (pos != nullptr) { + // Save index value as data to retrieve it after insertion + pos->data() = index; + hint = pos->full_cell(); + } else { + std::cout << "NULLPTR" << std::endl; + } } // -------------------------------------------------------------------------------------------- // structure to retrieve CGAL points from vertex handle - one vertex handle per point. @@ -270,9 +279,7 @@ class Alpha_complex { v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) v.push_back(get_point_(vertex)); - Point_d c = kernel_.construct_circumcenter_d_object()(v.cbegin(), v.cend()); - FT r = kernel_.squared_distance_d_object()(c, v[0]); - cache_.emplace_back(std::move(c), std::move(r)); + cache_.emplace_back(kernel_.get_sphere(v.cbegin(), v.cend())); } return cache_[k]; } @@ -282,13 +289,13 @@ class Alpha_complex { auto radius(SimplicialComplexForAlpha& cplx, typename SimplicialComplexForAlpha::Simplex_handle s) { auto k = cplx.key(s); if(k!=cplx.null_key()) - return old_cache_[k].second; + return kernel_.get_squared_radius(old_cache_[k]); // Using a transform_range is slower, currently. thread_local std::vector v; v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) v.push_back(get_point_(vertex)); - return kernel_.compute_squared_radius_d_object()(v.cbegin(), v.cend()); + return kernel_.get_squared_radius(v.cbegin(), v.cend()); } public: @@ -322,9 +329,9 @@ class Alpha_complex { bool exact = false, bool default_filtration_value = false) { // From SimplicialComplexForAlpha type required to insert into a simplicial complex (with or without subfaces). - typedef typename SimplicialComplexForAlpha::Vertex_handle Vertex_handle; - typedef typename SimplicialComplexForAlpha::Simplex_handle Simplex_handle; - typedef std::vector Vector_vertex; + using Vertex_handle = typename SimplicialComplexForAlpha::Vertex_handle; + using Simplex_handle = typename SimplicialComplexForAlpha::Simplex_handle; + using Vector_vertex = std::vector; if (triangulation_ == nullptr) { std::cerr << "Alpha_complex cannot create_complex from a NULL triangulation\n"; @@ -416,8 +423,8 @@ class Alpha_complex { template void propagate_alpha_filtration(SimplicialComplexForAlpha& complex, Simplex_handle f_simplex) { // From SimplicialComplexForAlpha type required to assign filtration values. - typedef typename SimplicialComplexForAlpha::Filtration_value Filtration_value; - typedef typename SimplicialComplexForAlpha::Vertex_handle Vertex_handle; + using Filtration_value = typename SimplicialComplexForAlpha::Filtration_value; + using Vertex_handle = typename SimplicialComplexForAlpha::Vertex_handle; // ### Foreach Tau face of Sigma for (auto f_boundary : complex.boundary_simplex_range(f_simplex)) { @@ -450,7 +457,8 @@ class Alpha_complex { while(shortiter != enditer && *longiter == *shortiter) { ++longiter; ++shortiter; } Vertex_handle extra = *longiter; auto const& cache=get_cache(complex, f_boundary); - bool is_gab = kernel_.squared_distance_d_object()(cache.first, get_point_(extra)) >= cache.second; + bool is_gab = kernel_.get_squared_distance(kernel_.get_circumcenter(cache), get_point_(extra)) >= + kernel_.get_squared_radius(cache); #ifdef DEBUG_TRACES std::clog << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << extra << std::endl; #endif // DEBUG_TRACES diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h new file mode 100644 index 00000000..87604ec4 --- /dev/null +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -0,0 +1,137 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#ifndef ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ +#define ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ + +#include // For EXACT or SAFE version +#include // For FAST version +#include // for CGAL_VERSION_NR + +#include // for EIGEN_VERSION_AT_LEAST + +#include // for std::make_pair + +// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10 +#if CGAL_VERSION_NR < 1041101000 +# error Alpha_complex is only available for CGAL >= 4.11 +#endif + +#if !EIGEN_VERSION_AT_LEAST(3,1,0) +# error Alpha_complex is only available for Eigen3 >= 3.1.0 installed with CGAL +#endif + +namespace Gudhi { + +namespace alpha_complex { + +template < typename Kernel, bool Weighted = false > +class Alpha_kernel_d { +}; + +// Unweighted Kernel_d version +template < typename Kernel > +class Alpha_kernel_d { + private: + // Kernel for functions access. + Kernel kernel_; + public: + // Fake type for compilation to succeed (cf. std::conditional in Alpha_complex.h) + using Weighted_point_d = void; + using Point_d = typename Kernel::Point_d; + // Numeric type of coordinates in the kernel + using FT = typename Kernel::FT; + // Sphere is a pair of point and squared radius. + using Sphere = typename std::pair; + + int get_dimension(const Point_d& p0) const { + return kernel_.point_dimension_d_object()(p0); + } + + template + Sphere get_sphere(PointIterator begin, PointIterator end) const { + Point_d c = kernel_.construct_circumcenter_d_object()(begin, end); + FT r = kernel_.squared_distance_d_object()(c, *begin); + return std::make_pair(std::move(c), std::move(r)); + } + + template + FT get_squared_radius(PointIterator begin, PointIterator end) const { + return kernel_.compute_squared_radius_d_object()(begin, end); + } + + FT get_squared_radius(const Sphere& sph) const { + return sph.second; + } + + template + Point get_circumcenter(const Sphere& sph) const { + return sph.first; + } + + template + FT get_squared_distance(const Point& first, const Point& second) const { + return kernel_.squared_distance_d_object()(first, second); + } +}; + +// Weighted Kernel_d version +template < typename Kernel > +class Alpha_kernel_d { + private: + // Kernel for functions access. + Kernel kernel_; + public: + // Fake type for compilation to succeed (cf. std::conditional in Alpha_complex.h) + using Point_d = void; + using Weighted_point_d = typename Kernel::Weighted_point_d; + using Bare_point_d = typename Kernel::Point_d; + // Numeric type of coordinates in the kernel + using FT = typename Kernel::FT; + // Sphere is a weighted point (point + weight [= squared radius]). + using Sphere = Weighted_point_d; + + int get_dimension(const Weighted_point_d& p0) const { + return kernel_.point_dimension_d_object()(p0.point()); + } + + template + Sphere get_sphere(PointIterator begin, PointIterator end) const { + return kernel_.power_center_d_object()(begin, end); + } + + template + FT get_squared_radius(PointIterator begin, PointIterator end) const { + Sphere sph = get_sphere(begin, end); + return sph.weight(); + } + + FT get_squared_radius(const Sphere& sph) const { + return sph.weight(); + } + + template + Point get_circumcenter(const Sphere& sph) const { + return sph.point(); + } + + template + FT get_squared_distance(const Point& first, const Point& second) const { + return kernel_.power_distance_d_object()(first, second); + } +}; + +} // namespace alpha_complex + +namespace alphacomplex = alpha_complex; + +} // namespace Gudhi + +#endif // ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ \ No newline at end of file diff --git a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp new file mode 100644 index 00000000..70b65aad --- /dev/null +++ b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp @@ -0,0 +1,132 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "alpha_kernel_d" +#include +#include + +#include +#include +#include + +#include +#include +#include // for std::pair + +#include +#include + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epeck_d< CGAL::Dynamic_dimension_tag > Exact_kernel_d; +// Use static dimension_tag for the user not to be able to set dimension +typedef CGAL::Epeck_d< CGAL::Dimension_tag<4> > Exact_kernel_s; +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Inexact_kernel_d; +// Use static dimension_tag for the user not to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Inexact_kernel_s; +// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter + +typedef boost::mpl::list list_of_kernel_variants; + +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_dimension, TestedKernel, list_of_kernel_variants) { + Gudhi::alpha_complex::Alpha_kernel_d kernel; + std::vector p0 {0., 1., 2., 3.}; + typename TestedKernel::Point_d p0_d(p0.begin(), p0.end()); + + std::clog << "Dimension is " << kernel.get_dimension(p0_d) << std::endl; + BOOST_CHECK(kernel.get_dimension(p0_d) == 4); + + Gudhi::alpha_complex::Alpha_kernel_d w_kernel; + typename TestedKernel::Weighted_point_d w_p0_d(p0_d, 10.); + + std::clog << "Dimension is " << w_kernel.get_dimension(w_p0_d) << std::endl; + BOOST_CHECK(w_kernel.get_dimension(w_p0_d) == 4); +} + +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_sphere, TestedKernel, list_of_kernel_variants) { + using Unweighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d; + // Sphere: (x-1)² + (y-1)² + z² + t² = 1 + // At least 5 points for a 3-sphere + std::vector p0 {1., 0., 0., 0.}; + std::vector p1 {0., 1., 0., 0.}; + std::vector p2 {1., 1., 1., 0.}; + std::vector p3 {1., 1., 0., 1.}; + std::vector p4 {1., 1., -1., 0.}; + + using Point_d = typename Unweighted_kernel::Point_d; + std::vector unw_pts; + unw_pts.push_back(Point_d(p0.begin(), p0.end())); + unw_pts.push_back(Point_d(p1.begin(), p1.end())); + unw_pts.push_back(Point_d(p2.begin(), p2.end())); + unw_pts.push_back(Point_d(p3.begin(), p3.end())); + unw_pts.push_back(Point_d(p4.begin(), p4.end())); + + Unweighted_kernel kernel; + auto unw_sphere = kernel.get_sphere(unw_pts.cbegin(), unw_pts.cend()); + + std::clog << "Center is " << unw_sphere.first << " - squared radius is " << unw_sphere.second << std::endl; + + using Weighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d; + + using Weighted_point_d = typename Weighted_kernel::Weighted_point_d; + using Bare_point_d = typename Weighted_kernel::Bare_point_d; + std::vector w_pts; + w_pts.push_back(Weighted_point_d(Bare_point_d(p0.begin(), p0.end()), 0.)); + w_pts.push_back(Weighted_point_d(Bare_point_d(p1.begin(), p1.end()), 0.)); + w_pts.push_back(Weighted_point_d(Bare_point_d(p2.begin(), p2.end()), 0.)); + w_pts.push_back(Weighted_point_d(Bare_point_d(p3.begin(), p3.end()), 0.)); + w_pts.push_back(Weighted_point_d(Bare_point_d(p4.begin(), p4.end()), 0.)); + + Weighted_kernel w_kernel; + auto w_sphere = w_kernel.get_sphere(w_pts.cbegin(), w_pts.cend()); + + std::clog << "Center is " << w_sphere.point() << " - squared radius is " << w_sphere.weight() << std::endl; + + CGAL::NT_converter cast_to_double; + // The results shall be the same with weights = 0. + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(unw_sphere.second), cast_to_double(w_sphere.weight())); + BOOST_CHECK(unw_sphere.first == w_sphere.point()); + + auto unw_sq_rd = kernel.get_squared_radius(unw_pts.cbegin(), unw_pts.cend()); + std::clog << "Squared radius is " << unw_sq_rd << std::endl; + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(unw_sphere.second), cast_to_double(unw_sq_rd)); + auto w_sq_rd = w_kernel.get_squared_radius(w_pts.cbegin(), w_pts.cend()); + std::clog << "Squared radius is " << w_sq_rd << std::endl; + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(w_sphere.weight()), cast_to_double(w_sq_rd)); +} + + +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_distance, TestedKernel, list_of_kernel_variants) { + using Unweighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d; + + std::vector p0 {1., 0., 0., 0.}; + std::vector p1 {0., 1., 0., 0.}; + + using Point_d = typename Unweighted_kernel::Point_d; + Unweighted_kernel kernel; + auto dist_01 = kernel.get_squared_distance(Point_d(p0.begin(), p0.end()), Point_d(p1.begin(), p1.end())); + std::clog << "Distance is " << dist_01 << std::endl; + + using Weighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d; + + using Weighted_point_d = typename Weighted_kernel::Weighted_point_d; + using Bare_point_d = typename Weighted_kernel::Bare_point_d; + std::vector w_pts; + + Weighted_kernel w_kernel; + auto w_dist_01 = w_kernel.get_squared_distance(Weighted_point_d(Bare_point_d(p0.begin(), p0.end()), 0.), + Weighted_point_d(Bare_point_d(p1.begin(), p1.end()), 0.)); + std::clog << "Distance is " << w_dist_01 << std::endl; + + CGAL::NT_converter cast_to_double; + // The results shall be the same with weights = 0. + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(dist_01), cast_to_double(w_dist_01)); +} diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index fe4b23e4..bd61c0d8 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -10,13 +10,17 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Alpha_complex_test_unit ${CGAL_LIBRARY}) add_executable ( Delaunay_complex_test_unit Delaunay_complex_unit_test.cpp ) target_link_libraries(Delaunay_complex_test_unit ${CGAL_LIBRARY}) + add_executable ( Alpha_kernel_d_test_unit Alpha_kernel_d_unit_test.cpp ) + target_link_libraries(Alpha_kernel_d_test_unit ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES}) target_link_libraries(Delaunay_complex_test_unit ${TBB_LIBRARIES}) + target_link_libraries(Alpha_kernel_d_test_unit ${TBB_LIBRARIES}) endif() gudhi_add_boost_test(Alpha_complex_test_unit) gudhi_add_boost_test(Delaunay_complex_test_unit) + gudhi_add_boost_test(Alpha_kernel_d_test_unit) add_executable ( Alpha_complex_3d_test_unit Alpha_complex_3d_unit_test.cpp ) target_link_libraries(Alpha_complex_3d_test_unit ${CGAL_LIBRARY}) -- cgit v1.2.3 From 9922407fe6f5d8872522157555c3573e95930ac3 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 7 Sep 2020 10:31:11 +0200 Subject: Fix compilation error and test with 0. weights --- src/Alpha_complex/example/CMakeLists.txt | 4 +++- .../example/Weighted_alpha_complex_from_points.cpp | 14 +++++++------- .../include/gudhi/Alpha_complex/Alpha_kernel_d.h | 11 ++++------- 3 files changed, 14 insertions(+), 15 deletions(-) diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 08eb979e..17dc896c 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -28,6 +28,8 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Alpha_complex_example_fast_from_off_32 COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt") + add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $) + if (DIFF_PATH) # Do not forget to copy test results files in current binary dir file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) @@ -47,7 +49,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) set_tests_properties(Alpha_complex_example_fast_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_32) endif() - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp index 19a04282..05858084 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -18,13 +18,13 @@ int main() { // Init of a list of points // ---------------------------------------------------------------------------- Vector_of_points points; - points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 1.)); - points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 1.)); - points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 1.)); - points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 1.)); - points.push_back(Weighted_point(Bare_point(0.0, 14.0), 1.)); - points.push_back(Weighted_point(Bare_point(2.0, 19.0), 1.)); - points.push_back(Weighted_point(Bare_point(9.0, 17.0), 1.)); + points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 0.)); + points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 0.)); + points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 0.)); + points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 0.)); + points.push_back(Weighted_point(Bare_point(0.0, 14.0), 0.)); + points.push_back(Weighted_point(Bare_point(2.0, 19.0), 0.)); + points.push_back(Weighted_point(Bare_point(9.0, 17.0), 0.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index 87604ec4..a3e3845a 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -71,8 +71,7 @@ class Alpha_kernel_d { return sph.second; } - template - Point get_circumcenter(const Sphere& sph) const { + auto get_circumcenter(const Sphere& sph) const { return sph.first; } @@ -117,13 +116,11 @@ class Alpha_kernel_d { return sph.weight(); } - template - Point get_circumcenter(const Sphere& sph) const { - return sph.point(); + auto get_circumcenter(const Sphere& sph) const { + return sph; } - template - FT get_squared_distance(const Point& first, const Point& second) const { + FT get_squared_distance(const Weighted_point_d& first, const Weighted_point_d& second) const { return kernel_.power_distance_d_object()(first, second); } }; -- cgit v1.2.3 From 05c9c0060ec8ff4cbf8619ff74724c2eea426d84 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 8 Sep 2020 16:43:36 +0200 Subject: CMake > 3.5 to use Boost targets. Compile only what is available from boost targets --- CMakeLists.txt | 2 +- src/Alpha_complex/utilities/CMakeLists.txt | 128 +++++++++++---------- src/Bottleneck_distance/example/CMakeLists.txt | 20 ++-- src/CMakeLists.txt | 2 +- src/Cech_complex/benchmark/CMakeLists.txt | 15 +-- src/Cech_complex/example/CMakeLists.txt | 15 +-- src/Cech_complex/test/CMakeLists.txt | 3 - src/Cech_complex/utilities/CMakeLists.txt | 19 +-- src/Collapse/utilities/CMakeLists.txt | 62 +++++----- src/Persistent_cohomology/benchmark/CMakeLists.txt | 14 ++- src/Persistent_cohomology/example/CMakeLists.txt | 79 +++++++------ src/Rips_complex/utilities/CMakeLists.txt | 67 ++++++----- src/Simplex_tree/example/CMakeLists.txt | 14 ++- src/Witness_complex/utilities/CMakeLists.txt | 36 +++--- src/cmake/modules/GUDHI_modules.cmake | 7 +- .../modules/GUDHI_third_party_libraries.cmake | 39 +------ src/common/doc/installation.h | 8 +- src/python/doc/installation.rst | 2 +- 18 files changed, 267 insertions(+), 265 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 8b82036b..4257a025 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 3.1) +cmake_minimum_required(VERSION 3.5) project(GUDHIdev) diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index f0ddfc2c..1e7dc1dd 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -1,80 +1,82 @@ project(Alpha_complex_utilities) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options) + if (TARGET Boost::program_options) + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) + target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options) - if (TBB_FOUND) - target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(NAME Alpha_complex_utilities_safe_alpha_complex_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "safe.pers") - add_test(NAME Alpha_complex_utilities_fast_alpha_complex_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "fast.pers" "-f") - add_test(NAME Alpha_complex_utilities_exact_alpha_complex_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e") - if (DIFF_PATH) - add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH} - "exact.pers" "safe.pers") - set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS - "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") - - add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH} - "fast.pers" "safe.pers") - set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS - "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") + if (TBB_FOUND) + target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Alpha_complex_utilities_safe_alpha_complex_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "safe.pers") + add_test(NAME Alpha_complex_utilities_fast_alpha_complex_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "fast.pers" "-f") + add_test(NAME Alpha_complex_utilities_exact_alpha_complex_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e") + if (DIFF_PATH) + add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH} + "exact.pers" "safe.pers") + set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS + "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") + add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH} + "fast.pers" "safe.pers") + set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS + "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") + endif() + + install(TARGETS alpha_complex_persistence DESTINATION bin) endif() - - install(TARGETS alpha_complex_persistence DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) if (NOT CGAL_VERSION VERSION_LESS 4.11.0) - add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options) - if (TBB_FOUND) - target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) + if (TARGET Boost::program_options) + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options) + if (TBB_FOUND) + target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) - add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "safe_3d.pers") + add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "safe_3d.pers") - add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e") + add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e") - add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f") - - if (DIFF_PATH) - add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH} - "exact_3d.pers" "safe_3d.pers") - set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS - "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") - add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH} - "fast_3d.pers" "safe_3d.pers") - set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS - "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") - endif() + add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f") - add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" - "-p" "2" "-m" "0") + if (DIFF_PATH) + add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH} + "exact_3d.pers" "safe_3d.pers") + set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS + "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") + add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH} + "fast_3d.pers" "safe_3d.pers") + set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS + "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") + endif() - add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" - "-p" "2" "-m" "0") + add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" + "-p" "2" "-m" "0") - add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" - "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" - "-p" "2" "-m" "0" "-e") - - install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" + "-p" "2" "-m" "0") + add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" + "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" + "-p" "2" "-m" "0" "-e") + + install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + endif() endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 9839c59d..d16ea6e5 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -12,14 +12,16 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance Boost::program_options) + if (TARGET Boost::program_options) + add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance Boost::program_options) - if (TBB_FOUND) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) - endif(TBB_FOUND) - - add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck - COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") + if (TBB_FOUND) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) + endif(TBB_FOUND) + + add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") + endif() endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 9e4d78ac..cc230531 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 3.1) +cmake_minimum_required(VERSION 3.5) project(GUDHI) diff --git a/src/Cech_complex/benchmark/CMakeLists.txt b/src/Cech_complex/benchmark/CMakeLists.txt index c04bca53..bc54c0f3 100644 --- a/src/Cech_complex/benchmark/CMakeLists.txt +++ b/src/Cech_complex/benchmark/CMakeLists.txt @@ -1,12 +1,13 @@ -cmake_minimum_required(VERSION 2.6) project(Cech_complex_benchmark) # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) -add_executable(cech_complex_benchmark cech_complex_benchmark.cpp) -target_link_libraries(cech_complex_benchmark Boost::filesystem) - -if (TBB_FOUND) - target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES}) -endif() +if(TARGET Boost::filesystem) + add_executable(cech_complex_benchmark cech_complex_benchmark.cpp) + target_link_libraries(cech_complex_benchmark Boost::filesystem) + + if (TBB_FOUND) + target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES}) + endif() +endif() \ No newline at end of file diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt index 98757988..1b08c7cb 100644 --- a/src/Cech_complex/example/CMakeLists.txt +++ b/src/Cech_complex/example/CMakeLists.txt @@ -1,13 +1,14 @@ -cmake_minimum_required(VERSION 2.6) project(Cech_complex_examples) -add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp ) -target_link_libraries(Cech_complex_example_step_by_step Boost::program_options) -if (TBB_FOUND) - target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES}) +if (TARGET Boost::program_options) + add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp ) + target_link_libraries(Cech_complex_example_step_by_step Boost::program_options) + if (TBB_FOUND) + target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES}) + endif() + add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-d" "3") endif() -add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-d" "3") add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp) if (TBB_FOUND) diff --git a/src/Cech_complex/test/CMakeLists.txt b/src/Cech_complex/test/CMakeLists.txt index db510af3..e6a2a18f 100644 --- a/src/Cech_complex/test/CMakeLists.txt +++ b/src/Cech_complex/test/CMakeLists.txt @@ -1,6 +1,3 @@ -cmake_minimum_required(VERSION 2.6) -project(Cech_complex_tests) - include(GUDHI_boost_test) add_executable ( Cech_complex_test_unit test_cech_complex.cpp ) diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt index 253d7304..b183c8d8 100644 --- a/src/Cech_complex/utilities/CMakeLists.txt +++ b/src/Cech_complex/utilities/CMakeLists.txt @@ -1,14 +1,15 @@ -cmake_minimum_required(VERSION 2.6) project(Cech_complex_utilities) -add_executable(cech_persistence cech_persistence.cpp) -target_link_libraries(cech_persistence Boost::program_options) +if (TARGET Boost::program_options) + add_executable(cech_persistence cech_persistence.cpp) + target_link_libraries(cech_persistence Boost::program_options) -if (TBB_FOUND) - target_link_libraries(cech_persistence ${TBB_LIBRARIES}) -endif() + if (TBB_FOUND) + target_link_libraries(cech_persistence ${TBB_LIBRARIES}) + endif() -add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") -install(TARGETS cech_persistence DESTINATION bin) + install(TARGETS cech_persistence DESTINATION bin) +endif() \ No newline at end of file diff --git a/src/Collapse/utilities/CMakeLists.txt b/src/Collapse/utilities/CMakeLists.txt index 97fef649..bce99e90 100644 --- a/src/Collapse/utilities/CMakeLists.txt +++ b/src/Collapse/utilities/CMakeLists.txt @@ -1,37 +1,37 @@ project(Collapse_utilities) if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) - - # From a point cloud - add_executable ( point_cloud_edge_collapse_rips_persistence point_cloud_edge_collapse_rips_persistence.cpp ) - target_link_libraries(point_cloud_edge_collapse_rips_persistence Boost::program_options) - - if (TBB_FOUND) - target_link_libraries(point_cloud_edge_collapse_rips_persistence ${TBB_LIBRARIES}) - endif() - add_test(NAME Edge_collapse_utilities_point_cloud_rips_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "off_results.pers") - - install(TARGETS point_cloud_edge_collapse_rips_persistence DESTINATION bin) - - # From a distance matrix - add_executable ( distance_matrix_edge_collapse_rips_persistence distance_matrix_edge_collapse_rips_persistence.cpp ) - target_link_libraries(distance_matrix_edge_collapse_rips_persistence Boost::program_options) - - if (TBB_FOUND) - target_link_libraries(distance_matrix_edge_collapse_rips_persistence ${TBB_LIBRARIES}) - endif() - add_test(NAME Edge_collapse_utilities_distance_matrix_rips_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/distance_matrix/tore3D_1307_distance_matrix.csv" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "csv_results.pers") - - install(TARGETS distance_matrix_edge_collapse_rips_persistence DESTINATION bin) - - if (DIFF_PATH) - add_test(Edge_collapse_utilities_diff_persistence ${DIFF_PATH} - "off_results.pers" "csv_results.pers") - set_tests_properties(Edge_collapse_utilities_diff_persistence PROPERTIES DEPENDS - "Edge_collapse_utilities_point_cloud_rips_persistence;Edge_collapse_utilities_distance_matrix_rips_persistence") - + if (TARGET Boost::program_options) + # From a point cloud + add_executable ( point_cloud_edge_collapse_rips_persistence point_cloud_edge_collapse_rips_persistence.cpp ) + target_link_libraries(point_cloud_edge_collapse_rips_persistence Boost::program_options) + + if (TBB_FOUND) + target_link_libraries(point_cloud_edge_collapse_rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Edge_collapse_utilities_point_cloud_rips_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "off_results.pers") + + install(TARGETS point_cloud_edge_collapse_rips_persistence DESTINATION bin) + + # From a distance matrix + add_executable ( distance_matrix_edge_collapse_rips_persistence distance_matrix_edge_collapse_rips_persistence.cpp ) + target_link_libraries(distance_matrix_edge_collapse_rips_persistence Boost::program_options) + + if (TBB_FOUND) + target_link_libraries(distance_matrix_edge_collapse_rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Edge_collapse_utilities_distance_matrix_rips_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/distance_matrix/tore3D_1307_distance_matrix.csv" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "csv_results.pers") + + install(TARGETS distance_matrix_edge_collapse_rips_persistence DESTINATION bin) + + if (DIFF_PATH) + add_test(Edge_collapse_utilities_diff_persistence ${DIFF_PATH} + "off_results.pers" "csv_results.pers") + set_tests_properties(Edge_collapse_utilities_diff_persistence PROPERTIES DEPENDS + "Edge_collapse_utilities_point_cloud_rips_persistence;Edge_collapse_utilities_distance_matrix_rips_persistence") + endif() endif() endif() \ No newline at end of file diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt index f38cc543..ad8dc84b 100644 --- a/src/Persistent_cohomology/benchmark/CMakeLists.txt +++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt @@ -2,11 +2,13 @@ project(Persistent_cohomology_benchmark) if(GMP_FOUND) if(GMPXX_FOUND) - add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp ) - target_link_libraries(performance_rips_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) - if (TBB_FOUND) - target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - file(COPY "${CMAKE_SOURCE_DIR}/data/points/Kl.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + if (TARGET Boost::program_options) + add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp ) + target_link_libraries(performance_rips_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + if (TBB_FOUND) + target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + file(COPY "${CMAKE_SOURCE_DIR}/data/points/Kl.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + endif() endif(GMPXX_FOUND) endif(GMP_FOUND) diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 4c08cd68..d6a92ed6 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -1,46 +1,58 @@ project(Persistent_cohomology_examples) add_executable(plain_homology plain_homology.cpp) +if (TBB_FOUND) + target_link_libraries(plain_homology ${TBB_LIBRARIES}) +endif() +add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $) +install(TARGETS plain_homology DESTINATION bin) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) - -add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) -target_link_libraries(rips_persistence_step_by_step Boost::program_options) - -add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp) -target_link_libraries(rips_persistence_via_boundary_matrix Boost::program_options) - -add_executable(persistence_from_file persistence_from_file.cpp) -target_link_libraries(persistence_from_file Boost::program_options) - if (TBB_FOUND) - target_link_libraries(plain_homology ${TBB_LIBRARIES}) target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) - target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) endif() - -add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $) add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $ "1" "0") -add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") -add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") -add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0") -add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") - -install(TARGETS plain_homology DESTINATION bin) install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin) -install(TARGETS rips_persistence_step_by_step DESTINATION bin) -install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin) -install(TARGETS persistence_from_file DESTINATION bin) + +if(TARGET Boost::program_options) + add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) + target_link_libraries(rips_persistence_step_by_step Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + install(TARGETS rips_persistence_step_by_step DESTINATION bin) +endif() + +if(TARGET Boost::program_options) + add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp) + target_link_libraries(rips_persistence_via_boundary_matrix Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") + install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin) +endif() + +if(TARGET Boost::program_options) + add_executable(persistence_from_file persistence_from_file.cpp) + target_link_libraries(persistence_from_file Boost::program_options) + if (TBB_FOUND) + target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $ + "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0") + add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $ + "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") + install(TARGETS persistence_from_file DESTINATION bin) +endif() if(GMP_FOUND) - if(GMPXX_FOUND) + if(GMPXX_FOUND) + if(TARGET Boost::program_options) add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) target_link_libraries(rips_multifield_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) @@ -50,19 +62,16 @@ if(GMP_FOUND) add_test(NAME Persistent_cohomology_example_multifield_2_71 COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "2" "-q" "71") install(TARGETS rips_multifield_persistence DESTINATION bin) - endif(GMPXX_FOUND) + endif() + endif(GMPXX_FOUND) endif(GMP_FOUND) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable(custom_persistence_sort custom_persistence_sort.cpp) target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY}) - if (TBB_FOUND) target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $) - install(TARGETS custom_persistence_sort DESTINATION bin) - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index d2448d7b..2081f142 100644 --- a/src/Rips_complex/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -1,34 +1,45 @@ project(Rips_complex_utilities) -add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) -target_link_libraries(rips_distance_matrix_persistence Boost::program_options) - -add_executable(rips_persistence rips_persistence.cpp) -target_link_libraries(rips_persistence Boost::program_options) - -add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp) -target_link_libraries(rips_correlation_matrix_persistence Boost::system Boost::program_options) - -add_executable(sparse_rips_persistence sparse_rips_persistence.cpp) -target_link_libraries(sparse_rips_persistence Boost::program_options) +if(TARGET Boost::program_options) + add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) + target_link_libraries(rips_distance_matrix_persistence Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $ + "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") + install(TARGETS rips_distance_matrix_persistence DESTINATION bin) +endif() -if (TBB_FOUND) - target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence ${TBB_LIBRARIES}) - target_link_libraries(rips_correlation_matrix_persistence ${TBB_LIBRARIES}) - target_link_libraries(sparse_rips_persistence ${TBB_LIBRARIES}) +if(TARGET Boost::program_options) + add_executable(rips_persistence rips_persistence.cpp) + target_link_libraries(rips_persistence Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + install(TARGETS rips_persistence DESTINATION bin) endif() -add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $ - "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") -add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") -add_test(NAME Rips_complex_utility_from_rips_correlation_matrix COMMAND $ - "${CMAKE_SOURCE_DIR}/data/correlation_matrix/lower_triangular_correlation_matrix.csv" "-c" "0.3" "-d" "3" "-p" "3" "-m" "0") -add_test(NAME Sparse_rips_complex_utility_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-e" "0.5" "-m" "0.2" "-d" "3" "-p" "2") +if(TARGET Boost::program_options) + add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp) + target_link_libraries(rips_correlation_matrix_persistence Boost::system Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_correlation_matrix_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Rips_complex_utility_from_rips_correlation_matrix COMMAND $ + "${CMAKE_SOURCE_DIR}/data/correlation_matrix/lower_triangular_correlation_matrix.csv" "-c" "0.3" "-d" "3" "-p" "3" "-m" "0") + install(TARGETS rips_correlation_matrix_persistence DESTINATION bin) +endif() -install(TARGETS rips_distance_matrix_persistence DESTINATION bin) -install(TARGETS rips_persistence DESTINATION bin) -install(TARGETS rips_correlation_matrix_persistence DESTINATION bin) -install(TARGETS sparse_rips_persistence DESTINATION bin) +if(TARGET Boost::program_options) + add_executable(sparse_rips_persistence sparse_rips_persistence.cpp) + target_link_libraries(sparse_rips_persistence Boost::program_options) + if (TBB_FOUND) + target_link_libraries(sparse_rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Sparse_rips_complex_utility_on_tore_3D COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-e" "0.5" "-m" "0.2" "-d" "3" "-p" "2") + install(TARGETS sparse_rips_persistence DESTINATION bin) +endif() diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index a0aabee2..73b2c6f9 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -34,13 +34,15 @@ if(GMP_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0) endif() if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp ) - target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES}) + if(TARGET Boost::program_options) + add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp ) + target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES}) + endif() + add_test(NAME Simplex_tree_example_cech_complex_cgal_mini_sphere_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" -r 0.3 -d 3) endif() - add_test(NAME Simplex_tree_example_cech_complex_cgal_mini_sphere_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" -r 0.3 -d 3) endif () add_executable ( Simplex_tree_example_graph_expansion_with_blocker graph_expansion_with_blocker.cpp ) diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt index d986d2d1..60fea0b4 100644 --- a/src/Witness_complex/utilities/CMakeLists.txt +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -2,26 +2,26 @@ project(Witness_complex_utilities) # CGAL and Eigen3 are required for Euclidean version of Witness if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - - add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp ) - target_link_libraries(Witness_complex_strong_witness_persistence Boost::program_options) + if(TARGET Boost::program_options) + add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_strong_witness_persistence Boost::program_options) - add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) - target_link_libraries(Witness_complex_weak_witness_persistence Boost::program_options) + add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) + target_link_libraries(Witness_complex_weak_witness_persistence Boost::program_options) - if (TBB_FOUND) - target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) - target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES}) - endif() - - add_test(NAME Witness_complex_strong_test_torus_persistence - COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") - add_test(NAME Witness_complex_weak_test_torus_persistence - COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + if (TBB_FOUND) + target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES}) + endif() - install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin) - install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin) + add_test(NAME Witness_complex_strong_test_torus_persistence + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + add_test(NAME Witness_complex_weak_test_torus_persistence + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin) + endif() endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake index aab1dd08..ccaf1ac5 100644 --- a/src/cmake/modules/GUDHI_modules.cmake +++ b/src/cmake/modules/GUDHI_modules.cmake @@ -30,7 +30,12 @@ if (WITH_GUDHI_EXAMPLE) set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};example") endif() if (WITH_GUDHI_TEST) - set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test") + # All tests are using boost tests + if(TARGET Boost::unit_test_framework) + set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test") + else() + message("++ WITH_GUDHI_TEST but no TARGET Boost::unit_test_framework") + endif() endif() if (WITH_GUDHI_UTILITIES) set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};utilities") diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index a56a2756..489f3de5 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -1,42 +1,11 @@ # This files manage third party libraries required by GUDHI -find_package(Boost 1.56.0 REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread) +find_package(Boost 1.56.0 QUIET OPTIONAL_COMPONENTS system thread filesystem unit_test_framework program_options) -if(NOT Boost_FOUND) +# Boost_FOUND is not reliable +if(NOT Boost_VERSION) message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") -endif(NOT Boost_FOUND) - -# cf. https://cliutils.gitlab.io/modern-cmake/chapters/packages/Boost.html -# This is needed if your Boost version is newer than your CMake version -# or if you have an old version of CMake (<3.5) -if(NOT TARGET Boost::program_options) - add_library(Boost::program_options IMPORTED INTERFACE) - set_property(TARGET Boost::program_options PROPERTY - INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) - set_property(TARGET Boost::program_options PROPERTY - INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) -endif() -if(NOT TARGET Boost::filesystem) - add_library(Boost::filesystem IMPORTED INTERFACE) - set_property(TARGET Boost::filesystem PROPERTY - INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) - set_property(TARGET Boost::filesystem PROPERTY - INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) -endif() -if(NOT TARGET Boost::unit_test_framework) - add_library(Boost::unit_test_framework IMPORTED INTERFACE) - set_property(TARGET Boost::unit_test_framework PROPERTY - INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) - set_property(TARGET Boost::unit_test_framework PROPERTY - INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) -endif() -if(NOT TARGET Boost::system) - add_library(Boost::system IMPORTED INTERFACE) - set_property(TARGET Boost::system PROPERTY - INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) - set_property(TARGET Boost::system PROPERTY - INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) -endif() +endif(NOT Boost_VERSION) find_package(GMP) if(GMP_FOUND) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 6af645e2..9df1c2f0 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -6,7 +6,7 @@ * * \section compiling Compiling * The library uses c++14 and requires Boost ≥ 1.56.0 - * and CMake ≥ 3.1. + * and CMake ≥ 3.5. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * * \subsection utilities Utilities and examples @@ -17,8 +17,8 @@ cd build/ cmake -DCMAKE_BUILD_TYPE=Release .. make \endverbatim * By default, examples are disabled. You can activate their compilation with - * ccmake (on Linux and Mac OSX), - * cmake-gui (on Windows) or by modifying the + * ccmake (on Linux and Mac OSX), + * cmake-gui (on Windows) or by modifying the * cmake command as follows : \verbatim cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON .. make \endverbatim @@ -28,7 +28,7 @@ make \endverbatim * To install the library (headers and activated utilities), run the following command in a terminal: * \verbatim make install \endverbatim * This action may require to be in the sudoer or administrator of the machine in function of the operating system and - * of CMAKE_INSTALL_PREFIX. + * of CMAKE_INSTALL_PREFIX. * * \subsection testsuites Test suites * To test your build, run the following command in a terminal: diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 4cc31d5c..2f161d66 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -40,7 +40,7 @@ different, and in particular the `python/` subdirectory is actually `src/python/ there. The library uses c++14 and requires `Boost `_ :math:`\geq` 1.56.0, -`CMake `_ :math:`\geq` 3.1 to generate makefiles, +`CMake `_ :math:`\geq` 3.5 to generate makefiles, `NumPy `_, `Cython `_ and `pybind11 `_ to compile the GUDHI Python module. -- cgit v1.2.3 From e213f44cdf0b2e2cfa854789c5f14cbb5cb4ec96 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 8 Sep 2020 17:51:26 +0200 Subject: Remove boost::system --- src/Rips_complex/utilities/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index 2081f142..d8c8e0b8 100644 --- a/src/Rips_complex/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -24,7 +24,7 @@ endif() if(TARGET Boost::program_options) add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp) - target_link_libraries(rips_correlation_matrix_persistence Boost::system Boost::program_options) + target_link_libraries(rips_correlation_matrix_persistence Boost::program_options) if (TBB_FOUND) target_link_libraries(rips_correlation_matrix_persistence ${TBB_LIBRARIES}) endif() -- cgit v1.2.3 From c09f54487cc88eeb3afe1629ff8a3edc223df1eb Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 9 Sep 2020 11:17:02 +0200 Subject: Even if CGAL was requiring boost::thread no need to find it for gudhi. boost::thread removed from cgal on https://github.com/CGAL/cgal/commit/8a7d3fa --- src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 489f3de5..1fbc4244 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -1,6 +1,6 @@ # This files manage third party libraries required by GUDHI -find_package(Boost 1.56.0 QUIET OPTIONAL_COMPONENTS system thread filesystem unit_test_framework program_options) +find_package(Boost 1.56.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framework program_options) # Boost_FOUND is not reliable if(NOT Boost_VERSION) -- cgit v1.2.3 From 58d79c972198938c6f3655a40540903e08242b36 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 9 Sep 2020 17:37:01 +0200 Subject: Use cgal 5.1 as only boost header only --- Dockerfile_for_pip | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/Dockerfile_for_pip b/Dockerfile_for_pip index 8f60e37c..98668a04 100644 --- a/Dockerfile_for_pip +++ b/Dockerfile_for_pip @@ -14,23 +14,24 @@ RUN mkdir -p /opt/cmake \ && sh cmake-3.16.2-Linux-x86_64.sh --skip-license --prefix=/opt/cmake \ && rm -f cmake-3.16.2-Linux-x86_64.sh -RUN git clone -b boost-1.73.0 --depth 1 https://github.com/boostorg/boost.git \ - && cd boost \ - && git submodule update --init \ - && ./bootstrap.sh --with-libraries=filesystem,program_options,system,thread,test \ - && ./b2 headers \ - && ./b2 install \ +# yum install boost-devel installs boost 1.53 and copy is the only way to install headers only boost +RUN wget https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.gz \ + && tar xf boost_1_73_0.tar.gz \ + && cd boost_1_73_0 \ + && ./bootstrap.sh \ + && ls \ + && cp -r boost /usr/local/include/ \ && cd .. \ && rm -rf boost -RUN wget https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-5.0.2/CGAL-5.0.2.tar.xz \ - && tar xf CGAL-5.0.2.tar.xz \ +RUN wget https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz \ + && tar xf CGAL-5.1.tar.xz \ && mkdir build \ && cd build \ - && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.0.2/ \ + && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ && make install \ && cd .. \ - && rm -rf build CGAL-5.0.2 + && rm -rf build CGAL-5.1 ADD .github/build-requirements.txt / -- cgit v1.2.3 From 171ddab9b7a50f0303d7201fa547dbfb445f9698 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 11 Sep 2020 11:55:55 +0200 Subject: Requires CGAL >= 5.1. Fix is_gabriel computation --- src/Alpha_complex/example/CMakeLists.txt | 14 +++++++++----- .../example/Weighted_alpha_complex_from_points.cpp | 14 +++++++------- src/Alpha_complex/include/gudhi/Alpha_complex.h | 8 ++++++-- .../include/gudhi/Alpha_complex/Alpha_kernel_d.h | 17 ++++------------- src/Alpha_complex/test/CMakeLists.txt | 13 +++++++++---- 5 files changed, 35 insertions(+), 31 deletions(-) diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 17dc896c..1fc2330a 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -7,13 +7,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) add_executable ( Alpha_complex_example_fast_from_off Fast_alpha_complex_from_off.cpp ) target_link_libraries(Alpha_complex_example_fast_from_off ${CGAL_LIBRARY}) - add_executable ( Weighted_alpha_complex_example_from_points Weighted_alpha_complex_from_points.cpp ) - target_link_libraries(Weighted_alpha_complex_example_from_points ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) target_link_libraries(Alpha_complex_example_fast_from_off ${TBB_LIBRARIES}) - target_link_libraries(Weighted_alpha_complex_example_from_points ${TBB_LIBRARIES}) endif() add_test(NAME Alpha_complex_example_from_points COMMAND $) @@ -28,8 +25,6 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Alpha_complex_example_fast_from_off_32 COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt") - add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $) - if (DIFF_PATH) # Do not forget to copy test results files in current binary dir file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) @@ -69,3 +64,12 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) COMMAND $) endif(NOT CGAL_VERSION VERSION_LESS 4.11.0) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) + add_executable ( Weighted_alpha_complex_example_from_points Weighted_alpha_complex_from_points.cpp ) + target_link_libraries(Weighted_alpha_complex_example_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Weighted_alpha_complex_example_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $) +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp index 05858084..19a04282 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -18,13 +18,13 @@ int main() { // Init of a list of points // ---------------------------------------------------------------------------- Vector_of_points points; - points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 0.)); - points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 0.)); - points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 0.)); - points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 0.)); - points.push_back(Weighted_point(Bare_point(0.0, 14.0), 0.)); - points.push_back(Weighted_point(Bare_point(2.0, 19.0), 0.)); - points.push_back(Weighted_point(Bare_point(9.0, 17.0), 0.)); + points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 1.)); + points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 1.)); + points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 1.)); + points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 1.)); + points.push_back(Weighted_point(Bare_point(0.0, 14.0), 1.)); + points.push_back(Weighted_point(Bare_point(2.0, 19.0), 1.)); + points.push_back(Weighted_point(Bare_point(9.0, 17.0), 1.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 8e9fe773..4316d9bc 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -210,6 +210,11 @@ class Alpha_complex { << std::endl; #endif +#if CGAL_VERSION_NR < 1050101000 + // Make compilation fail if weighted and CGAL < 5.1 + static_assert(!Weighted, "Weighted Alpha_complex is only available for CGAL >= 5.1"); +#endif + auto first = std::begin(points); auto last = std::end(points); @@ -457,8 +462,7 @@ class Alpha_complex { while(shortiter != enditer && *longiter == *shortiter) { ++longiter; ++shortiter; } Vertex_handle extra = *longiter; auto const& cache=get_cache(complex, f_boundary); - bool is_gab = kernel_.get_squared_distance(kernel_.get_circumcenter(cache), get_point_(extra)) >= - kernel_.get_squared_radius(cache); + bool is_gab = kernel_.is_gabriel(cache, get_point_(extra)); #ifdef DEBUG_TRACES std::clog << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << extra << std::endl; #endif // DEBUG_TRACES diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index a3e3845a..b64e4f59 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -71,13 +71,8 @@ class Alpha_kernel_d { return sph.second; } - auto get_circumcenter(const Sphere& sph) const { - return sph.first; - } - - template - FT get_squared_distance(const Point& first, const Point& second) const { - return kernel_.squared_distance_d_object()(first, second); + bool is_gabriel(const Sphere& circumcenter, const Point_d& point) { + return kernel_.squared_distance_d_object()(circumcenter.first, point) >= circumcenter.second; } }; @@ -116,12 +111,8 @@ class Alpha_kernel_d { return sph.weight(); } - auto get_circumcenter(const Sphere& sph) const { - return sph; - } - - FT get_squared_distance(const Weighted_point_d& first, const Weighted_point_d& second) const { - return kernel_.power_distance_d_object()(first, second); + bool is_gabriel(const Sphere& circumcenter, const Weighted_point_d& point) { + return kernel_.power_distance_d_object()(circumcenter, point) >= 0; } }; diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index 71e4ea7c..837d2948 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -10,17 +10,13 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Alpha_complex_test_unit ${CGAL_LIBRARY}) add_executable ( Delaunay_complex_test_unit Delaunay_complex_unit_test.cpp ) target_link_libraries(Delaunay_complex_test_unit ${CGAL_LIBRARY}) - add_executable ( Alpha_kernel_d_test_unit Alpha_kernel_d_unit_test.cpp ) - target_link_libraries(Alpha_kernel_d_test_unit ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES}) target_link_libraries(Delaunay_complex_test_unit ${TBB_LIBRARIES}) - target_link_libraries(Alpha_kernel_d_test_unit ${TBB_LIBRARIES}) endif() gudhi_add_boost_test(Alpha_complex_test_unit) gudhi_add_boost_test(Delaunay_complex_test_unit) - gudhi_add_boost_test(Alpha_kernel_d_test_unit) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) @@ -47,3 +43,12 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) gudhi_add_boost_test(Weighted_periodic_alpha_complex_3d_test_unit) endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) + add_executable ( Alpha_kernel_d_test_unit Alpha_kernel_d_unit_test.cpp ) + target_link_libraries(Alpha_kernel_d_test_unit ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_kernel_d_test_unit ${TBB_LIBRARIES}) + endif() + gudhi_add_boost_test(Alpha_kernel_d_test_unit) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) \ No newline at end of file -- cgit v1.2.3 From d299e943d6fd07a58a270fe685dac7b5d5d23964 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 11 Sep 2020 14:35:39 +0200 Subject: fonction was renamed between 5.1 and 5.2 --- .../include/gudhi/Alpha_complex/Alpha_kernel_d.h | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index b64e4f59..a4824207 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -82,6 +82,7 @@ class Alpha_kernel_d { private: // Kernel for functions access. Kernel kernel_; + public: // Fake type for compilation to succeed (cf. std::conditional in Alpha_complex.h) using Point_d = void; @@ -98,7 +99,13 @@ class Alpha_kernel_d { template Sphere get_sphere(PointIterator begin, PointIterator end) const { + // power_center_d_object has been renamed between CGAL 5.1 and 5.2 +#if defined CGAL_VERSION_NR >= 1050101000 && defined CGAL_VERSION_NR < 1050201000 return kernel_.power_center_d_object()(begin, end); +#endif +#if CGAL_VERSION_NR >= 1050201000 + return kernel_.construct_power_sphere_d_object()(begin, end); +#endif } template @@ -112,7 +119,13 @@ class Alpha_kernel_d { } bool is_gabriel(const Sphere& circumcenter, const Weighted_point_d& point) { + // power_center_d_object has been renamed between CGAL 5.1 and 5.2 +#if defined CGAL_VERSION_NR >= 1050101000 && defined CGAL_VERSION_NR < 1050201000 return kernel_.power_distance_d_object()(circumcenter, point) >= 0; +#endif +#if CGAL_VERSION_NR >= 1050201000 + return kernel_.compute_power_product_d_object()(circumcenter, point) >= 0; +#endif } }; -- cgit v1.2.3 From 54e0cec31e556c88d9f8107394ad972883fdbbdf Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 11 Sep 2020 17:41:39 +0200 Subject: Add weighted ctor and its test --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 26 +++++++ src/Alpha_complex/test/CMakeLists.txt | 8 +++ .../test/Weighted_alpha_complex_unit_test.cpp | 82 ++++++++++++++++++++++ 3 files changed, 116 insertions(+) create mode 100644 src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 4316d9bc..00231e1c 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -31,6 +31,10 @@ #include // for EIGEN_VERSION_AT_LEAST +#include +#include +#include + #include #include #include @@ -179,6 +183,28 @@ class Alpha_complex { init_from_range(points); } + /** \brief Alpha_complex constructor from a list of points and weights. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * + * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d or Kernel::Weighted_point_d. + * + * @param[in] weights Range of points weights. Weights must be in Kernel::FT. + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a Kernel::Point_d. + */ + template + Alpha_complex(const InputPointRange& points, WeightRange weights) { + static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d"); + // FIXME: this test is only valid if we have a forward range + GUDHI_CHECK(boost::size(weights) == boost::size(points), + std::invalid_argument("Points number in range different from weights range number")); + auto weighted_points = boost::range::combine(points, weights) + | boost::adaptors::transformed([](auto const&t){return Point_d(boost::get<0>(t), boost::get<1>(t));}); + init_from_range(weighted_points); + } + /** \brief Alpha_complex destructor deletes the Delaunay triangulation. */ ~Alpha_complex() { diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index 837d2948..db5d840f 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -51,4 +51,12 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) target_link_libraries(Alpha_kernel_d_test_unit ${TBB_LIBRARIES}) endif() gudhi_add_boost_test(Alpha_kernel_d_test_unit) + + add_executable ( Weighted_alpha_complex_test_unit Weighted_alpha_complex_unit_test.cpp ) + target_link_libraries(Weighted_alpha_complex_test_unit ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Weighted_alpha_complex_test_unit ${TBB_LIBRARIES}) + endif() + gudhi_add_boost_test(Weighted_alpha_complex_test_unit) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) \ No newline at end of file diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp new file mode 100644 index 00000000..b4fc76de --- /dev/null +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -0,0 +1,82 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "weighted_alpha_complex" +#include +#include + +#include +#include + +#include // float comparison +#include +#include + +#include +#include +#include + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epeck_d< CGAL::Dynamic_dimension_tag > Exact_kernel_d; +// Use static dimension_tag for the user not to be able to set dimension +typedef CGAL::Epeck_d< CGAL::Dimension_tag<4> > Exact_kernel_s; +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Inexact_kernel_d; +// Use static dimension_tag for the user not to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Inexact_kernel_s; +// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter + +typedef boost::mpl::list list_of_kernel_variants; + +BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_kernel_variants) { + // Random points construction + using Point_d = typename Kernel::Point_d; + std::vector points; + std::uniform_real_distribution rd_pts(-10., 10.); + std::random_device rand_dev; + std::mt19937 rand_engine(rand_dev()); + for (int idx = 0; idx < 20; idx++) { + std::vector point {rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine)}; + points.emplace_back(Point_d(point.begin(), point.end())); + } + + // Alpha complex from points + Gudhi::alpha_complex::Alpha_complex alpha_complex_from_points(points); + Gudhi::Simplex_tree<> simplex; + BOOST_CHECK(alpha_complex_from_points.create_complex(simplex)); + std::clog << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::clog << std::endl; + } + + // Alpha complex from zero weighted points + std::vector weights(20, 0.); + Gudhi::alpha_complex::Alpha_complex alpha_complex_from_zero_weighted_points(points, weights); + Gudhi::Simplex_tree<> zw_simplex; + BOOST_CHECK(alpha_complex_from_zero_weighted_points.create_complex(zw_simplex)); + + std::clog << "Iterator on zero weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : zw_simplex.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : zw_simplex.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << zw_simplex.filtration(f_simplex) << "] "; + std::clog << std::endl; + } + + BOOST_CHECK(zw_simplex == simplex); +} \ No newline at end of file -- cgit v1.2.3 From 5e3871c2d99249bd7560faa4e1229d3b3751b0ff Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 14 Sep 2020 11:17:40 +0200 Subject: alpha_complex_persistence utils can use weighted points. Update Alpha_kernel_d_unit_test to work --- .../test/Alpha_kernel_d_unit_test.cpp | 28 ------ .../test/Weighted_alpha_complex_unit_test.cpp | 2 +- .../utilities/alpha_complex_persistence.cpp | 101 ++++++++++++++++----- src/Alpha_complex/utilities/alphacomplex.md | 7 ++ 4 files changed, 84 insertions(+), 54 deletions(-) diff --git a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp index 70b65aad..192834b3 100644 --- a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp @@ -102,31 +102,3 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_sphere, TestedKernel, list_of_kerne std::clog << "Squared radius is " << w_sq_rd << std::endl; GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(w_sphere.weight()), cast_to_double(w_sq_rd)); } - - -BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_distance, TestedKernel, list_of_kernel_variants) { - using Unweighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d; - - std::vector p0 {1., 0., 0., 0.}; - std::vector p1 {0., 1., 0., 0.}; - - using Point_d = typename Unweighted_kernel::Point_d; - Unweighted_kernel kernel; - auto dist_01 = kernel.get_squared_distance(Point_d(p0.begin(), p0.end()), Point_d(p1.begin(), p1.end())); - std::clog << "Distance is " << dist_01 << std::endl; - - using Weighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d; - - using Weighted_point_d = typename Weighted_kernel::Weighted_point_d; - using Bare_point_d = typename Weighted_kernel::Bare_point_d; - std::vector w_pts; - - Weighted_kernel w_kernel; - auto w_dist_01 = w_kernel.get_squared_distance(Weighted_point_d(Bare_point_d(p0.begin(), p0.end()), 0.), - Weighted_point_d(Bare_point_d(p1.begin(), p1.end()), 0.)); - std::clog << "Distance is " << w_dist_01 << std::endl; - - CGAL::NT_converter cast_to_double; - // The results shall be the same with weights = 0. - GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(dist_01), cast_to_double(w_dist_01)); -} diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index b4fc76de..57a57058 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -21,6 +21,7 @@ #include #include +#include #include #include @@ -32,7 +33,6 @@ typedef CGAL::Epeck_d< CGAL::Dimension_tag<4> > Exact_kernel_s; typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Inexact_kernel_d; // Use static dimension_tag for the user not to be able to set dimension typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Inexact_kernel_s; -// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter typedef boost::mpl::list list_of_kernel_variants; diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index e17831d9..e86b34e2 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -17,19 +17,82 @@ #include // to construct a simplex_tree from alpha complex #include +#include #include #include #include // for numeric_limits +#include +#include using Simplex_tree = Gudhi::Simplex_tree<>; using Filtration_value = Simplex_tree::Filtration_value; void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast, - std::string &output_file_diag, Filtration_value &alpha_square_max_value, + std::string &weight_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, Filtration_value &min_persistence); +template +std::vector read_off(const std::string &off_file_points) { + Gudhi::Points_off_reader off_reader(off_file_points); + if (!off_reader.is_valid()) { + std::cerr << "Alpha_complex - Unable to read file " << off_file_points << "\n"; + exit(-1); // ----- >> + } + return off_reader.get_point_cloud(); +} + +std::vector read_weight_file(const std::string &weight_file) { + std::vector weights; + // Read weights information from file + std::ifstream weights_ifstr(weight_file); + if (weights_ifstr.good()) { + double weight = 0.0; + // Attempt read the weight in a double format, return false if it fails + while (weights_ifstr >> weight) { + weights.push_back(weight); + } + } else { + std::cerr << "Unable to read weights file " << weight_file << std::endl; + exit(-1); + } + return weights; +} + +template +Simplex_tree create_simplex_tree(const std::string &off_file_points, const std::string &weight_file, + bool exact_version, Filtration_value alpha_square_max_value) { + Simplex_tree stree; + auto points = read_off(off_file_points); + + if (weight_file != std::string()) { + std::vector weights = read_weight_file(weight_file); + if (points.size() != weights.size()) { + std::cerr << "Alpha_complex - Inconsistency between number of points (" << points.size() + << ") and number of weights (" << weights.size() << ")" << "\n"; + exit(-1); // ----- >> + } + // Init of an alpha complex from an OFF file + Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(points, weights); + + if (!alpha_complex_from_file.create_complex(stree, alpha_square_max_value, exact_version)) { + std::cerr << "Alpha complex simplicial complex creation failed." << std::endl; + exit(-1); + } + } else { + // Init of an alpha complex from an OFF file + Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(points); + + if (!alpha_complex_from_file.create_complex(stree, alpha_square_max_value, exact_version)) { + std::cerr << "Alpha complex simplicial complex creation failed." << std::endl; + exit(-1); + } + } + return stree; +} + int main(int argc, char **argv) { + std::string weight_file; std::string off_file_points; std::string output_file_diag; bool exact_version = false; @@ -38,48 +101,34 @@ int main(int argc, char **argv) { int coeff_field_characteristic; Filtration_value min_persistence; - program_options(argc, argv, off_file_points, exact_version, fast_version, output_file_diag, alpha_square_max_value, - coeff_field_characteristic, min_persistence); + program_options(argc, argv, off_file_points, exact_version, fast_version, weight_file, output_file_diag, + alpha_square_max_value, coeff_field_characteristic, min_persistence); if ((exact_version) && (fast_version)) { std::cerr << "You cannot set the exact and the fast version." << std::endl; exit(-1); } - Simplex_tree simplex; + Simplex_tree stree; if (fast_version) { // WARNING : CGAL::Epick_d is fast but not safe (unlike CGAL::Epeck_d) // (i.e. when the points are on a grid) using Fast_kernel = CGAL::Epick_d; - - // Init of an alpha complex from an OFF file - Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(off_file_points); - - if (!alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { - std::cerr << "Fast Alpha complex simplicial complex creation failed." << std::endl; - exit(-1); - } + stree = create_simplex_tree(off_file_points, weight_file, exact_version, alpha_square_max_value); } else { using Kernel = CGAL::Epeck_d; - - // Init of an alpha complex from an OFF file - Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(off_file_points); - - if (!alpha_complex_from_file.create_complex(simplex, alpha_square_max_value, exact_version)) { - std::cerr << "Alpha complex simplicial complex creation failed." << std::endl; - exit(-1); - } + stree = create_simplex_tree(off_file_points, weight_file, exact_version, alpha_square_max_value); } // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::clog << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() - << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; + std::clog << "Simplicial complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() + << " simplices - " << stree.num_vertices() << " vertices." << std::endl; - std::clog << "Simplex_tree dim: " << simplex.dimension() << std::endl; + std::clog << "Simplex_tree dim: " << stree.dimension() << std::endl; // Compute the persistence diagram of the complex Gudhi::persistent_cohomology::Persistent_cohomology pcoh( - simplex); + stree); // initializes the coefficient field for homology pcoh.init_coefficients(coeff_field_characteristic); @@ -98,7 +147,7 @@ int main(int argc, char **argv) { } void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast, - std::string &output_file_diag, Filtration_value &alpha_square_max_value, + std::string &weight_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, Filtration_value &min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); @@ -111,6 +160,8 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool "To activate exact version of Alpha complex (default is false, not available if fast is set)")( "fast,f", po::bool_switch(&fast), "To activate fast version of Alpha complex (default is false, not available if exact is set)")( + "weight-file,w", po::value(&weight_file)->default_value(std::string()), + "Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")( "output-file,o", po::value(&output_file_diag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::clog")( "max-alpha-square-value,r", po::value(&alpha_square_max_value) diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index 527598a9..0d3c6027 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -46,6 +46,9 @@ for the Alpha complex construction. coefficient field Z/pZ for computing homology. * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +* `-w [ --weight-file ]` is the path to the file containing the weights of the +points (one value per line). +Default version is not weighted. * `-e [ --exact ]` for the exact computation version. * `-f [ --fast ]` for the fast computation version. @@ -58,6 +61,10 @@ to be recorded. Enter a negative value to see zero length intervals. N.B.: * Filtration values are alpha square values. +* Weights values are explained on CGAL +[dD Triangulations](https://doc.cgal.org/latest/Triangulation/index.html) +and +[Regular triangulation](https://doc.cgal.org/latest/Triangulation/index.html#title20) documentation. ## alpha_complex_3d_persistence ## -- cgit v1.2.3 From de39546182c20a69e45aa07830351f6e9d2e4b84 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 14 Sep 2020 17:27:40 +0200 Subject: Add but comment a test to compare dD and 3D alpha complex --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 2 - .../test/Weighted_alpha_complex_unit_test.cpp | 79 +++++++++++++++++++++- 2 files changed, 78 insertions(+), 3 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 00231e1c..e1aae2d4 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -267,8 +267,6 @@ class Alpha_complex { // Save index value as data to retrieve it after insertion pos->data() = index; hint = pos->full_cell(); - } else { - std::cout << "NULLPTR" << std::endl; } } // -------------------------------------------------------------------------------------------- diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index 57a57058..bf659ef7 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -79,4 +79,81 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_kerne } BOOST_CHECK(zw_simplex == simplex); -} \ No newline at end of file +} + +template +bool cgal_3d_point_sort (Point_d a,Point_d b) { + if (a[0] != b[0]) + return a[0] < b[0]; + if (a[1] != b[1]) + return a[1] < b[1]; + return a[2] < b[2]; +} + +/*BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { + // Random points construction + using Kernel_dD = CGAL::Epeck_d< CGAL::Dimension_tag<3> >; + using Bare_point_d = typename Kernel_dD::Point_d; + using Weighted_point_d = typename Kernel_dD::Weighted_point_d; + std::vector w_points_d; + + using Exact_weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; + using Bare_point_3 = typename Exact_weighted_alpha_complex_3d::Bare_point_3; + using Weighted_point_3 = typename Exact_weighted_alpha_complex_3d::Weighted_point_3; + std::vector w_points_3; + + std::uniform_real_distribution rd_pts(-10., 10.); + std::uniform_real_distribution rd_wghts(-0.5, 0.5); + std::random_device rand_dev; + std::mt19937 rand_engine(rand_dev()); + for (int idx = 0; idx < 20; idx++) { + std::vector point {rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine)}; + double weight = rd_wghts(rand_engine); + w_points_d.emplace_back(Weighted_point_d(Bare_point_d(point.begin(), point.end()), weight)); + w_points_3.emplace_back(Weighted_point_3(Bare_point_3(point[0], point[1], point[2]), weight)); + } + + // Weighted alpha complex for dD version + Gudhi::alpha_complex::Alpha_complex alpha_complex_dD_from_weighted_points(w_points_d); + Gudhi::Simplex_tree<> w_simplex_d; + BOOST_CHECK(alpha_complex_dD_from_weighted_points.create_complex(w_simplex_d)); + + std::clog << "Iterator on weighted alpha complex dD simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : w_simplex_d.filtration_simplex_range()) { + std::clog << " ( "; + std::vector points; + for (auto vertex : w_simplex_d.simplex_vertex_range(f_simplex)) { + points.emplace_back(alpha_complex_dD_from_weighted_points.get_point(vertex).point()); + } + std::sort (points.begin(), points.end(), cgal_3d_point_sort); + for (auto point : points) { + std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; + } + std::clog << ") -> " << "[" << w_simplex_d.filtration(f_simplex) << "] "; + std::clog << std::endl; + } + + // Weighted alpha complex for 3D version + Exact_weighted_alpha_complex_3d alpha_complex_3D_from_weighted_points(w_points_3); + Gudhi::Simplex_tree<> w_simplex_3; + BOOST_CHECK(alpha_complex_3D_from_weighted_points.create_complex(w_simplex_3)); + + std::clog << "Iterator on weighted alpha complex 3D simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : w_simplex_3.filtration_simplex_range()) { + std::clog << " ( "; + std::vector points; + for (auto vertex : w_simplex_3.simplex_vertex_range(f_simplex)) { + points.emplace_back(alpha_complex_3D_from_weighted_points.get_point(vertex).point()); + } + std::sort (points.begin(), points.end()); + for (auto point : points) { + std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; + } + std::clog << ") -> " << "[" << w_simplex_3.filtration(f_simplex) << "] "; + std::clog << std::endl; + } + + BOOST_CHECK(w_simplex_d == w_simplex_3); + +}*/ \ No newline at end of file -- cgit v1.2.3 From 53d09e2f7770f7e95d765d527712ef3c0758cf08 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 14 Sep 2020 21:35:23 +0200 Subject: Fix Alpha complex to have the same results than Alpha complex 3d --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 31 +++++++++++++++++++++++-- 1 file changed, 29 insertions(+), 2 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index e1aae2d4..f43cd071 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -60,6 +60,27 @@ namespace alpha_complex { template struct Is_Epeck_D { static const bool value = false; }; template struct Is_Epeck_D> { static const bool value = true; }; +template +struct Weight; + +template +struct Weight +{ + typename Kernel::FT operator()(const typename Kernel::Weighted_point_d& p) const + { + return p.weight(); + } +}; + +template +struct Weight +{ + typename Kernel::FT operator()(const typename Kernel::Point_d& p) const + { + return 0.; + } +}; + /** * \class Alpha_complex Alpha_complex.h gudhi/Alpha_complex.h * \brief Alpha complex data structure. @@ -404,6 +425,7 @@ class Alpha_complex { // -------------------------------------------------------------------------------------------- if (!default_filtration_value) { + CGAL::NT_converter cgal_converter; // -------------------------------------------------------------------------------------------- // ### For i : d -> 0 for (int decr_dim = triangulation_->maximal_dimension(); decr_dim >= 0; decr_dim--) { @@ -420,8 +442,7 @@ class Alpha_complex { #if CGAL_VERSION_NR >= 1050000000 if(exact) CGAL::exact(sqrad); #endif - CGAL::NT_converter cv; - alpha_complex_filtration = cv(sqrad); + alpha_complex_filtration = cgal_converter(sqrad); } complex.assign_filtration(f_simplex, alpha_complex_filtration); #ifdef DEBUG_TRACES @@ -431,6 +452,12 @@ class Alpha_complex { // No need to propagate further, unweighted points all have value 0 if (decr_dim > 1) propagate_alpha_filtration(complex, f_simplex); + // For weighted points, assign point weight as filtration value + if (Weighted && decr_dim == 0) { + Vertex_handle vertex = *(complex.simplex_vertex_range(f_simplex).begin()); + FT wght = Weight()(get_point(vertex)); + complex.assign_filtration(f_simplex, cgal_converter(wght)*(-1.)); + } } } old_cache_ = std::move(cache_); -- cgit v1.2.3 From 6db3b5db0f8b6dfae2b9b6eadb8bccdfdc613fb5 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 15 Sep 2020 13:45:37 +0200 Subject: This should be correct and efficient for 0-dimension weighted alpha --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index f43cd071..b66ec20d 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -436,8 +436,8 @@ class Alpha_complex { // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma) if (std::isnan(complex.filtration(f_simplex))) { Filtration_value alpha_complex_filtration = 0.0; - // No need to compute squared_radius on a single point - alpha is 0.0 - if (f_simplex_dim > 0) { + // No need to compute squared_radius on a non-weighted single point - alpha is 0.0 + if (Weighted || f_simplex_dim > 0) { auto const& sqrad = radius(complex, f_simplex); #if CGAL_VERSION_NR >= 1050000000 if(exact) CGAL::exact(sqrad); @@ -450,14 +450,8 @@ class Alpha_complex { #endif // DEBUG_TRACES } // No need to propagate further, unweighted points all have value 0 - if (decr_dim > 1) + if (decr_dim > !Weighted) propagate_alpha_filtration(complex, f_simplex); - // For weighted points, assign point weight as filtration value - if (Weighted && decr_dim == 0) { - Vertex_handle vertex = *(complex.simplex_vertex_range(f_simplex).begin()); - FT wght = Weight()(get_point(vertex)); - complex.assign_filtration(f_simplex, cgal_converter(wght)*(-1.)); - } } } old_cache_ = std::move(cache_); -- cgit v1.2.3 From 4dacc3d99bfc4a4d31088fe126090038156ab7a0 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 15 Sep 2020 16:56:17 +0200 Subject: Make Kernel available publicly for tests purpose --- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 622b10ee..4e5fc933 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -154,8 +154,10 @@ class Alpha_complex_3d { using Kernel = CGAL::Periodic_3_regular_triangulation_traits_3; }; + public: using Kernel = typename Kernel_3::Kernel; + private: using TdsVb = typename std::conditional, CGAL::Triangulation_ds_vertex_base_3<>>::type; -- cgit v1.2.3 From 019bc2dc28dd6db3b21a24354051fe3a4d2e1f77 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 15 Sep 2020 16:56:54 +0200 Subject: alpha complex persistence now requires cgal 5.1 --- src/Alpha_complex/utilities/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index f0ddfc2c..90e5734e 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -1,6 +1,6 @@ project(Alpha_complex_utilities) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options) @@ -27,7 +27,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) endif() install(TARGETS alpha_complex_persistence DESTINATION bin) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) -- cgit v1.2.3 From d6f68d20e975e0cd530cd15ca5f7f782550e6af4 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 15 Sep 2020 16:57:15 +0200 Subject: Test alpha complex dD versus 3d --- .../test/Weighted_alpha_complex_unit_test.cpp | 54 +++++++++++++++++----- 1 file changed, 43 insertions(+), 11 deletions(-) diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index bf659ef7..e8372656 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -19,6 +19,8 @@ #include // float comparison #include #include +#include +#include // for std::fabs #include #include @@ -90,7 +92,7 @@ bool cgal_3d_point_sort (Point_d a,Point_d b) { return a[2] < b[2]; } -/*BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { +BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { // Random points construction using Kernel_dD = CGAL::Epeck_d< CGAL::Dimension_tag<3> >; using Bare_point_d = typename Kernel_dD::Point_d; @@ -114,6 +116,12 @@ bool cgal_3d_point_sort (Point_d a,Point_d b) { w_points_3.emplace_back(Weighted_point_3(Bare_point_3(point[0], point[1], point[2]), weight)); } + // Structures necessary for comparison + using Points = std::vector>; + using Points_and_filtrations = std::map; + Points_and_filtrations pts_fltr_dD; + Points_and_filtrations pts_fltr_3d; + // Weighted alpha complex for dD version Gudhi::alpha_complex::Alpha_complex alpha_complex_dD_from_weighted_points(w_points_d); Gudhi::Simplex_tree<> w_simplex_d; @@ -121,17 +129,20 @@ bool cgal_3d_point_sort (Point_d a,Point_d b) { std::clog << "Iterator on weighted alpha complex dD simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : w_simplex_d.filtration_simplex_range()) { - std::clog << " ( "; - std::vector points; + Points points; for (auto vertex : w_simplex_d.simplex_vertex_range(f_simplex)) { - points.emplace_back(alpha_complex_dD_from_weighted_points.get_point(vertex).point()); + CGAL::NT_converter cgal_converter; + Bare_point_d pt = alpha_complex_dD_from_weighted_points.get_point(vertex).point(); + points.push_back({cgal_converter(pt[0]), cgal_converter(pt[1]), cgal_converter(pt[2])}); } - std::sort (points.begin(), points.end(), cgal_3d_point_sort); + std::clog << " ( "; + std::sort (points.begin(), points.end()); for (auto point : points) { std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; } std::clog << ") -> " << "[" << w_simplex_d.filtration(f_simplex) << "] "; std::clog << std::endl; + pts_fltr_dD[points] = w_simplex_d.filtration(f_simplex); } // Weighted alpha complex for 3D version @@ -141,19 +152,40 @@ bool cgal_3d_point_sort (Point_d a,Point_d b) { std::clog << "Iterator on weighted alpha complex 3D simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : w_simplex_3.filtration_simplex_range()) { - std::clog << " ( "; - std::vector points; + Points points; for (auto vertex : w_simplex_3.simplex_vertex_range(f_simplex)) { - points.emplace_back(alpha_complex_3D_from_weighted_points.get_point(vertex).point()); + Bare_point_3 pt = alpha_complex_3D_from_weighted_points.get_point(vertex).point(); + CGAL::NT_converter cgal_converter; + points.push_back({cgal_converter(pt[0]), cgal_converter(pt[1]), cgal_converter(pt[2])}); } + std::clog << " ( "; std::sort (points.begin(), points.end()); for (auto point : points) { std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; } std::clog << ") -> " << "[" << w_simplex_3.filtration(f_simplex) << "] "; std::clog << std::endl; + pts_fltr_3d[points] = w_simplex_d.filtration(f_simplex); } - BOOST_CHECK(w_simplex_d == w_simplex_3); - -}*/ \ No newline at end of file + // Compares structures + auto d3_itr = pts_fltr_3d.begin(); + auto dD_itr = pts_fltr_dD.begin(); + for (; d3_itr != pts_fltr_3d.end() && dD_itr != pts_fltr_dD.end(); ++d3_itr) { + if (d3_itr->first != dD_itr->first) { + for(auto point : d3_itr->first) + std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; + std::clog << " versus "; + for(auto point : dD_itr->first) + std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; + std::clog << std::endl; + BOOST_CHECK(false); + } + // I had to make a hard limit as it is converted from Kernel::FT + if (std::fabs(d3_itr->second - dD_itr->second) > 1e-5) { + std::clog << d3_itr->second << " versus " << dD_itr->second << " diff " << std::fabs(d3_itr->second - dD_itr->second) << std::endl; + BOOST_CHECK(false); + } + ++dD_itr; + } +} -- cgit v1.2.3 From cb68f3e4c8ce7724ccb693e5c67dd9928d12d84b Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 16 Sep 2020 12:39:00 +0200 Subject: Some documentation about weighted dD Alpha complex. Make examples 3d/dD consistents --- src/Alpha_complex/doc/Intro_alpha_complex.h | 35 +++++++++++++++++++++- .../Weighted_alpha_complex_3d_from_points.cpp | 4 +-- .../example/Weighted_alpha_complex_from_points.cpp | 16 +++++----- .../example/weightedalpha3dfrompoints_for_doc.txt | 4 +-- 4 files changed, 45 insertions(+), 14 deletions(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 60da7169..f14adee6 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -22,6 +22,17 @@ namespace alpha_complex { * * @{ * +
+Table of Contents + +
+ * \section definition Definition * * Alpha_complex is a simplicial complex @@ -146,6 +157,28 @@ namespace alpha_complex { * `SimplicialComplexForAlpha::prune_above_filtration()`). * In the following example, the value is given by the user as argument of the program. * + * \section weightedversion Weighted specific version + * Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 5.1.0. + * For performances reasons, it is advised to use \ref eigen ≥ 3.5.8 and \ref cgal ≥ 5.2.0 + * A weighted version for Alpha complex is available (cf. Alpha_complex). + * + * This example builds the CGAL weighted alpha shapes from a small molecule, and initializes the alpha complex with + * it. This example is taken from CGAL 3d + * weighted alpha shapes. + * + * Then, it is asked to display information about the alpha complex. + * + * \include Alpha_complex/Weighted_alpha_complex_from_points.cpp + * + * When launching: + * + * \code $> ./Weighted_alpha_complex_example_from_points + * \endcode + * + * the program output is: + * + * \include Alpha_complex/weightedalpha3dfrompoints_for_doc.txt + * * * \section offexample Example from OFF file * @@ -166,7 +199,7 @@ namespace alpha_complex { * \include Alpha_complex/alphaoffreader_for_doc_32.txt * * - * \section weighted3dexample 3d specific example + * \section weighted3dexample 3d specific version * * A specific module for Alpha complex is available in 3d (cf. Alpha_complex_3d) and allows to construct standard, * weighted, periodic or weighted and periodic versions of alpha complexes. Alpha values computation can be diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index c044194e..74f0cf30 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -34,10 +34,10 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::clog << "Alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + std::clog << "Weighted alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; - std::clog << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : simplex.filtration_simplex_range()) { std::clog << " ( "; for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp index 19a04282..d49d3e93 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -8,23 +8,21 @@ #include // Explicit dimension 2 Epeck_d kernel -using Kernel = CGAL::Epeck_d< CGAL::Dimension_tag<2> >; +using Kernel = CGAL::Epeck_d< CGAL::Dimension_tag<3> >; using Bare_point = Kernel::Point_d; using Weighted_point = Kernel::Weighted_point_d; using Vector_of_points = std::vector; int main() { // ---------------------------------------------------------------------------- - // Init of a list of points + // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- Vector_of_points points; - points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 1.)); - points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 1.)); - points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 1.)); - points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 1.)); - points.push_back(Weighted_point(Bare_point(0.0, 14.0), 1.)); - points.push_back(Weighted_point(Bare_point(2.0, 19.0), 1.)); - points.push_back(Weighted_point(Bare_point(9.0, 17.0), 1.)); + points.push_back(Weighted_point(Bare_point(1, -1, -1), 4.)); + points.push_back(Weighted_point(Bare_point(-1, 1, -1), 4.)); + points.push_back(Weighted_point(Bare_point(-1, -1, 1), 4.)); + points.push_back(Weighted_point(Bare_point(1, 1, 1), 4.)); + points.push_back(Weighted_point(Bare_point(2, 2, 2), 1.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt index 7a09998d..f0695f1a 100644 --- a/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt +++ b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt @@ -1,5 +1,5 @@ -Alpha complex is of dimension 3 - 29 simplices - 5 vertices. -Iterator on alpha complex simplices in the filtration order, with [filtration value]: +Weighted alpha complex is of dimension 3 - 29 simplices - 5 vertices. +Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]: ( 0 ) -> [-4] ( 1 ) -> [-4] ( 2 ) -> [-4] -- cgit v1.2.3 From 282934d4f51acac046c04f752534a6a900880df9 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 16 Sep 2020 12:43:35 +0200 Subject: Add weighted in toc --- src/Alpha_complex/doc/Intro_alpha_complex.h | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index f14adee6..b04562e1 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -28,6 +28,7 @@ Table of Contents
  • Definition
  • Example from points
  • Create complex algorithm
    • +
  • Weighted specific version
  • Example from OFF file
  • 3d specific version
    • @@ -214,14 +215,7 @@ Table of Contents * * \include Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * - * When launching: - * - * \code $> ./Alpha_complex_example_weighted_3d_from_points - * \endcode - * - * the program output is: - * - * \include Alpha_complex/weightedalpha3dfrompoints_for_doc.txt + * The results will be the same as in \ref weightedversion . * */ /** @} */ // end defgroup alpha_complex -- cgit v1.2.3 From 837ffddda60d3f389184fe167710f74ad8adf36b Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 17 Sep 2020 09:37:25 +0200 Subject: Some documentation for weighted version --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 7 ++++--- src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h | 8 ++++++++ 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index b66ec20d..1d395bd8 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -132,17 +132,18 @@ class Alpha_complex { using Triangulation = typename std::conditional, CGAL::Delaunay_triangulation>::type; + /** \brief CGAL kernel container for computations in function of the weighted or not characteristics.*/ using A_kernel_d = Alpha_kernel_d; // Numeric type of coordinates in the kernel using FT = typename A_kernel_d::FT; - /** \brief If Weighted, the weighted point is cached (point + weight [= squared radius]), - * else a pair of point and squared radius is cached. + /** \brief Sphere is a std::pair (aka. circurmcenter and squared radius). + * If Weighted, Sphere is a Kernel::Weighted_point_d (aka. circurmcenter and the weight value is the squared radius). */ using Sphere = typename A_kernel_d::Sphere; - /** \brief A point in Euclidean space.*/ + /** \brief A point, or a weighted point in Euclidean space.*/ using Point_d = typename std::conditional::type; diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index a4824207..e3567a6d 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -32,6 +32,14 @@ namespace Gudhi { namespace alpha_complex { +/** + * \class Alpha_kernel_d + * \brief Alpha complex kernel container. + * + * \details + * The Alpha complex kernel container stores CGAL Kernel and dispatch basics computations in function of the weighted + * or not version of the Alpha complex. + */ template < typename Kernel, bool Weighted = false > class Alpha_kernel_d { }; -- cgit v1.2.3 From 77c0275031f47bb94f94d02d63182178e46f6570 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 17 Sep 2020 10:24:30 +0200 Subject: Remove useless code --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 1d395bd8..be0a5b95 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -60,27 +60,6 @@ namespace alpha_complex { template struct Is_Epeck_D { static const bool value = false; }; template struct Is_Epeck_D> { static const bool value = true; }; -template -struct Weight; - -template -struct Weight -{ - typename Kernel::FT operator()(const typename Kernel::Weighted_point_d& p) const - { - return p.weight(); - } -}; - -template -struct Weight -{ - typename Kernel::FT operator()(const typename Kernel::Point_d& p) const - { - return 0.; - } -}; - /** * \class Alpha_complex Alpha_complex.h gudhi/Alpha_complex.h * \brief Alpha complex data structure. -- cgit v1.2.3 From 8afdbebe27effb0a9c184a153b645dd85aa0415b Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 18 Sep 2020 13:08:37 +0200 Subject: Fix #if cgal_version --- .../include/gudhi/Alpha_complex/Alpha_kernel_d.h | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index e3567a6d..a6760645 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -108,18 +108,16 @@ class Alpha_kernel_d { template Sphere get_sphere(PointIterator begin, PointIterator end) const { // power_center_d_object has been renamed between CGAL 5.1 and 5.2 -#if defined CGAL_VERSION_NR >= 1050101000 && defined CGAL_VERSION_NR < 1050201000 +#if CGAL_VERSION_NR < 1050201000 return kernel_.power_center_d_object()(begin, end); -#endif -#if CGAL_VERSION_NR >= 1050201000 +#else return kernel_.construct_power_sphere_d_object()(begin, end); #endif } template FT get_squared_radius(PointIterator begin, PointIterator end) const { - Sphere sph = get_sphere(begin, end); - return sph.weight(); + return get_sphere(begin, end).weight(); } FT get_squared_radius(const Sphere& sph) const { @@ -128,10 +126,9 @@ class Alpha_kernel_d { bool is_gabriel(const Sphere& circumcenter, const Weighted_point_d& point) { // power_center_d_object has been renamed between CGAL 5.1 and 5.2 -#if defined CGAL_VERSION_NR >= 1050101000 && defined CGAL_VERSION_NR < 1050201000 +#if CGAL_VERSION_NR < 1050201000 return kernel_.power_distance_d_object()(circumcenter, point) >= 0; -#endif -#if CGAL_VERSION_NR >= 1050201000 +#else return kernel_.compute_power_product_d_object()(circumcenter, point) >= 0; #endif } -- cgit v1.2.3 From c6619e0207abf0fb5198b66a8d8f00f975c3da84 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 18 Sep 2020 16:27:49 +0200 Subject: Use CGAL 5.1 by default on dockers. Update next release --- .github/next_release.md | 6 +++--- Dockerfile_for_circleci_image | 10 +++++++++- Dockerfile_for_pip | 8 ++++---- Dockerfile_gudhi_installation | 12 ++++++++++++ 4 files changed, 28 insertions(+), 8 deletions(-) diff --git a/.github/next_release.md b/.github/next_release.md index cd2376eb..190f8408 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,13 +1,13 @@ We are pleased to announce the release 3.4.0 of the GUDHI library. -As a major new feature, the GUDHI library now offers ... +As a major new feature, the GUDHI library now offers dD weighted alpha complex, ... We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.4.0.tar.gz). Below is a list of changes made since GUDHI 3.3.0: -- [Module](link) - - ... +- [Alpha complex](https://gudhi.inria.fr/doc/latest/group__alpha__complex.html) + - the C++ weighted version for alpha complex is now available in dimension D. - [Module](link) - ... diff --git a/Dockerfile_for_circleci_image b/Dockerfile_for_circleci_image index 87f57071..ec1b8ff8 100644 --- a/Dockerfile_for_circleci_image +++ b/Dockerfile_for_circleci_image @@ -41,7 +41,6 @@ RUN apt-get install -y make \ libgmp3-dev \ libmpfr-dev \ libtbb-dev \ - libcgal-dev \ locales \ python3 \ python3-pip \ @@ -51,6 +50,15 @@ RUN apt-get install -y make \ pkg-config \ curl +RUN curl -LO "https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz" \ + && tar xf CGAL-5.1.tar.xz \ + && mkdir build \ + && cd build \ + && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ + && make install \ + && cd .. \ + && rm -rf build CGAL-5.1 + ADD .github/build-requirements.txt / ADD .github/test-requirements.txt / diff --git a/Dockerfile_for_pip b/Dockerfile_for_pip index 8f60e37c..83c6d684 100644 --- a/Dockerfile_for_pip +++ b/Dockerfile_for_pip @@ -23,14 +23,14 @@ RUN git clone -b boost-1.73.0 --depth 1 https://github.com/boostorg/boost.git \ && cd .. \ && rm -rf boost -RUN wget https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-5.0.2/CGAL-5.0.2.tar.xz \ - && tar xf CGAL-5.0.2.tar.xz \ +RUN wget https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz \ + && tar xf CGAL-5.1.tar.xz \ && mkdir build \ && cd build \ - && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.0.2/ \ + && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ && make install \ && cd .. \ - && rm -rf build CGAL-5.0.2 + && rm -rf build CGAL-5.1 ADD .github/build-requirements.txt / diff --git a/Dockerfile_gudhi_installation b/Dockerfile_gudhi_installation index 92430fce..ebd21f8d 100644 --- a/Dockerfile_gudhi_installation +++ b/Dockerfile_gudhi_installation @@ -23,6 +23,9 @@ ENV LANG en_US.UTF-8 ENV LANGUAGE en_US:en ENV LC_ALL en_US.UTF-8 +# Update again +RUN apt-get update + # Required for Gudhi compilation RUN apt-get install -y make \ g++ \ @@ -47,6 +50,15 @@ RUN apt-get install -y make \ pkg-config \ curl +RUN curl -LO "https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz" \ + && tar xf CGAL-5.1.tar.xz \ + && mkdir build \ + && cd build \ + && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ + && make install \ + && cd .. \ + && rm -rf build CGAL-5.1 + RUN pip3 install \ numpy \ matplotlib \ -- cgit v1.2.3 From 4186971033ee43821905cac53791bf074751d3af Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 28 Sep 2020 09:15:52 +0200 Subject: code review: Let the exception propagate --- src/python/gudhi/simplex_tree.pyx | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 5250937b..5043c621 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -295,13 +295,9 @@ cdef class SimplexTree: """ cdef pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] it = self.get_ptr().get_boundary_iterators(simplex) - try: - while it.first != it.second: - yield self.get_ptr().get_simplex_and_filtration(dereference(it.first)) - preincrement(it.first) - except RuntimeError: - print("simplex not found - cannot find boundaries") - + while it.first != it.second: + yield self.get_ptr().get_simplex_and_filtration(dereference(it.first)) + preincrement(it.first) def remove_maximal_simplex(self, simplex): """This function removes a given maximal N-simplex from the simplicial -- 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(-) 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 0c843fd01f0cd1ccff92c8ed40e989b3fbf8f1e9 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 28 Sep 2020 09:56:44 +0200 Subject: code review: Simplify recursivity --- src/Simplex_tree/include/gudhi/Simplex_tree.h | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 5afd0e23..85d6c3b0 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1677,14 +1677,7 @@ class Simplex_tree { * @param[in] min_dim The minimal dimension. Default value is 0. */ 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); - } - if (has_children(&simplex)) { - rec_reset_filtration(simplex.second.children(), filt_value, min_dim - 1); - } - } + rec_reset_filtration(&root_, filt_value, min_dim); clear_filtration(); // Drop the cache. } -- cgit v1.2.3 From e7b7947adf13ec1dcb8c126a4373fa29baaecb63 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 29 Sep 2020 13:23:56 +0200 Subject: Added tests for wasserstein distance with tensorflow --- .../modules/GUDHI_third_party_libraries.cmake | 1 + src/python/CMakeLists.txt | 8 +++++++ src/python/doc/installation.rst | 5 +++++ src/python/test/test_wasserstein_with_tensors.py | 25 ++++++++++++++++++++++ 4 files changed, 39 insertions(+) create mode 100755 src/python/test/test_wasserstein_with_tensors.py diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 1fbc4244..9dadac4f 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -155,6 +155,7 @@ if( PYTHONINTERP_FOUND ) find_python_module("pykeops") find_python_module("eagerpy") find_python_module_no_version("hnswlib") + find_python_module("tensorflow") endif() if(NOT GUDHI_PYTHON_PATH) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 4f26481e..cc71503f 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -103,6 +103,9 @@ if(PYTHONINTERP_FOUND) if(EAGERPY_FOUND) add_gudhi_debug_info("EagerPy version ${EAGERPY_VERSION}") endif() + if(TENSORFLOW_FOUND) + add_gudhi_debug_info("TensorFlow version ${TENSORFLOW_VERSION}") + endif() set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") @@ -501,6 +504,11 @@ if(PYTHONINTERP_FOUND) endif() add_gudhi_py_test(test_wasserstein_barycenter) endif() + if(OT_FOUND) + if(TENSORFLOW_FOUND AND EAGERPY_FOUND) + add_gudhi_py_test(test_wasserstein_with_tensors) + endif() + endif() # Representations if(SKLEARN_FOUND AND MATPLOTLIB_FOUND) diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 2f161d66..66efe45a 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -394,6 +394,11 @@ mathematics, science, and engineering. :class:`~gudhi.point_cloud.knn.KNearestNeighbors` can use the Python package `SciPy `_ as a backend if explicitly requested. +TensorFlow +---------- + +`TensorFlow `_ is currently only used in some automatic differentiation tests. + Bug reports and contributions ***************************** diff --git a/src/python/test/test_wasserstein_with_tensors.py b/src/python/test/test_wasserstein_with_tensors.py new file mode 100755 index 00000000..8957705d --- /dev/null +++ b/src/python/test/test_wasserstein_with_tensors.py @@ -0,0 +1,25 @@ +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Mathieu Carriere + + Copyright (C) 2020 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +from gudhi.wasserstein import wasserstein_distance as pot +import numpy as np + +def test_wasserstein_distance_grad_tensorflow(): + import tensorflow as tf + + with tf.GradientTape() as tape: + diag4 = tf.convert_to_tensor(tf.Variable(initial_value=np.array([[0., 10.]]), trainable=True)) + diag5 = tf.convert_to_tensor(tf.Variable(initial_value=np.array([[1., 11.], [3., 4.]]), trainable=True)) + dist45 = pot(diag4, diag5, internal_p=1, order=1, enable_autodiff=True) + assert dist45 == 3. + + grads = tape.gradient(dist45, [diag4, diag5]) + assert np.array_equal(grads[0].values, [[-1., -1.]]) + assert np.array_equal(grads[1].values, [[1., 1.], [-1., 1.]]) \ No newline at end of file -- cgit v1.2.3 From b1b0e9afcaf0e282115dddad7b958b6ec7a94a41 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 29 Sep 2020 14:33:28 +0200 Subject: code review: inconsistency between code and comment --- src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 74f0cf30..a8d00272 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -9,7 +9,7 @@ // Complexity = FAST, weighted = true, periodic = false using Weighted_alpha_complex_3d = - Gudhi::alpha_complex::Alpha_complex_3d; + Gudhi::alpha_complex::Alpha_complex_3d; using Bare_point = Weighted_alpha_complex_3d::Bare_point_3; using Weighted_point = Weighted_alpha_complex_3d::Weighted_point_3; -- cgit v1.2.3 From 6f2ec5ee6572351d3aee5f559ef4cf7ad03bf914 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 29 Sep 2020 15:00:53 +0200 Subject: doc review: fix eigen version and period --- src/Alpha_complex/doc/Intro_alpha_complex.h | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index b04562e1..78486ad6 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -160,7 +160,8 @@ Table of Contents * * \section weightedversion Weighted specific version * Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 5.1.0. - * For performances reasons, it is advised to use \ref eigen ≥ 3.5.8 and \ref cgal ≥ 5.2.0 + * For performances reasons, it is advised to use \ref eigen ≥ 3.3.5 and \ref cgal ≥ 5.2.0. + * * A weighted version for Alpha complex is available (cf. Alpha_complex). * * This example builds the CGAL weighted alpha shapes from a small molecule, and initializes the alpha complex with -- cgit v1.2.3 From b08a52c3b625e70d1c69834df7253e115da7946e Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 29 Sep 2020 15:35:11 +0200 Subject: code review: use of std::conditional_t c++14 helper --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index be0a5b95..e8bf1f74 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -101,15 +101,16 @@ template, bool Weighte class Alpha_complex { public: /** \brief Geometric traits class that provides the geometric types and predicates needed by the triangulations.*/ - using Geom_traits = typename std::conditional, - Kernel>::type; + using Geom_traits = std::conditional_t, Kernel>; + // Add an int in TDS to save point index in the structure using TDS = CGAL::Triangulation_data_structure, CGAL::Triangulation_full_cell >; + /** \brief A (Weighted or not) Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ - using Triangulation = typename std::conditional, - CGAL::Delaunay_triangulation>::type; + using Triangulation = std::conditional_t, + CGAL::Delaunay_triangulation>; /** \brief CGAL kernel container for computations in function of the weighted or not characteristics.*/ using A_kernel_d = Alpha_kernel_d; @@ -123,8 +124,7 @@ class Alpha_complex { using Sphere = typename A_kernel_d::Sphere; /** \brief A point, or a weighted point in Euclidean space.*/ - using Point_d = typename std::conditional::type; + using Point_d = std::conditional_t; private: // Vertex_iterator type from CGAL. -- cgit v1.2.3 From 44473bcd93892c7034fa21599509d4271f2d8bb2 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 29 Sep 2020 17:16:02 +0200 Subject: doc review: rephrase non contiguous vertices --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index e8bf1f74..38201027 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -171,7 +171,8 @@ class Alpha_complex { /** \brief Alpha_complex constructor from a list of points. * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * The vertices may be not contiguous as some points may be discarded in the triangulation (duplicate points, + * weighted hidden point, ...). * * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d or Kernel::Weighted_point_d. * @@ -186,7 +187,8 @@ class Alpha_complex { /** \brief Alpha_complex constructor from a list of points and weights. * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * The vertices may be not contiguous as some points may be discarded in the triangulation (duplicate points, + * weighted hidden point, ...). * * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d or Kernel::Weighted_point_d. * -- cgit v1.2.3 From dab93ead76f1435f6b74937ef0377aafb0517439 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 29 Sep 2020 17:53:34 +0200 Subject: doc review: Modify ctor with points and weights documentation --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 38201027..a692dbc6 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -176,8 +176,8 @@ class Alpha_complex { * * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d or Kernel::Weighted_point_d. * - * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a Kernel::Point_d or Kernel::Weighted_point_d. + * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a + * Kernel::Point_d or Kernel::Weighted_point_d. */ template Alpha_complex(const InputPointRange& points) @@ -190,12 +190,12 @@ class Alpha_complex { * The vertices may be not contiguous as some points may be discarded in the triangulation (duplicate points, * weighted hidden point, ...). * - * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d or Kernel::Weighted_point_d. + * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d. * * @param[in] weights Range of points weights. Weights must be in Kernel::FT. * - * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a Kernel::Point_d. + * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a + * Kernel::Point_d. */ template Alpha_complex(const InputPointRange& points, WeightRange weights) { -- cgit v1.2.3 From c1b317640f81fefff7f7a774b239957fb632fa43 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 30 Sep 2020 09:18:36 +0200 Subject: code review: emplace_back versus push_back --- .../Weighted_alpha_complex_3d_from_points.cpp | 10 +++++----- .../example/Weighted_alpha_complex_from_points.cpp | 10 +++++----- src/Alpha_complex/include/gudhi/Alpha_complex.h | 6 +++--- src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp | 20 ++++++++++---------- .../utilities/alpha_complex_persistence.cpp | 2 +- 5 files changed, 24 insertions(+), 24 deletions(-) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index a8d00272..09431d6e 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -18,11 +18,11 @@ int main(int argc, char **argv) { // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- std::vector weighted_points; - weighted_points.push_back(Weighted_point(Bare_point(1, -1, -1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(-1, 1, -1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(-1, -1, 1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(1, 1, 1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(2, 2, 2), 1.)); + weighted_points.emplace_back(Bare_point(1, -1, -1), 4.); + weighted_points.emplace_back(Bare_point(-1, 1, -1), 4.); + weighted_points.emplace_back(Bare_point(-1, -1, 1), 4.); + weighted_points.emplace_back(Bare_point(1, 1, 1), 4.); + weighted_points.emplace_back(Bare_point(2, 2, 2), 1.); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp index d49d3e93..d1f3e436 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -18,11 +18,11 @@ int main() { // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- Vector_of_points points; - points.push_back(Weighted_point(Bare_point(1, -1, -1), 4.)); - points.push_back(Weighted_point(Bare_point(-1, 1, -1), 4.)); - points.push_back(Weighted_point(Bare_point(-1, -1, 1), 4.)); - points.push_back(Weighted_point(Bare_point(1, 1, 1), 4.)); - points.push_back(Weighted_point(Bare_point(2, 2, 2), 1.)); + points.emplace_back(Bare_point(1, -1, -1), 4.); + points.emplace_back(Bare_point(-1, 1, -1), 4.); + points.emplace_back(Bare_point(-1, -1, 1), 4.); + points.emplace_back(Bare_point(1, 1, 1), 4.); + points.emplace_back(Bare_point(2, 2, 2), 1.); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index a692dbc6..4f8e3d54 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -310,7 +310,7 @@ class Alpha_complex { thread_local std::vector v; v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) - v.push_back(get_point_(vertex)); + v.emplace_back(get_point_(vertex)); cache_.emplace_back(kernel_.get_sphere(v.cbegin(), v.cend())); } return cache_[k]; @@ -326,7 +326,7 @@ class Alpha_complex { thread_local std::vector v; v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) - v.push_back(get_point_(vertex)); + v.emplace_back(get_point_(vertex)); return kernel_.get_squared_radius(v.cbegin(), v.cend()); } @@ -394,7 +394,7 @@ class Alpha_complex { std::clog << " " << (*vit)->data(); #endif // DEBUG_TRACES // Vector of vertex construction for simplex_tree structure - vertexVector.push_back((*vit)->data()); + vertexVector.emplace_back((*vit)->data()); } } #ifdef DEBUG_TRACES diff --git a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp index 192834b3..6eae103d 100644 --- a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp @@ -63,11 +63,11 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_sphere, TestedKernel, list_of_kerne using Point_d = typename Unweighted_kernel::Point_d; std::vector unw_pts; - unw_pts.push_back(Point_d(p0.begin(), p0.end())); - unw_pts.push_back(Point_d(p1.begin(), p1.end())); - unw_pts.push_back(Point_d(p2.begin(), p2.end())); - unw_pts.push_back(Point_d(p3.begin(), p3.end())); - unw_pts.push_back(Point_d(p4.begin(), p4.end())); + unw_pts.emplace_back(p0.begin(), p0.end()); + unw_pts.emplace_back(p1.begin(), p1.end()); + unw_pts.emplace_back(p2.begin(), p2.end()); + unw_pts.emplace_back(p3.begin(), p3.end()); + unw_pts.emplace_back(p4.begin(), p4.end()); Unweighted_kernel kernel; auto unw_sphere = kernel.get_sphere(unw_pts.cbegin(), unw_pts.cend()); @@ -79,11 +79,11 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_sphere, TestedKernel, list_of_kerne using Weighted_point_d = typename Weighted_kernel::Weighted_point_d; using Bare_point_d = typename Weighted_kernel::Bare_point_d; std::vector w_pts; - w_pts.push_back(Weighted_point_d(Bare_point_d(p0.begin(), p0.end()), 0.)); - w_pts.push_back(Weighted_point_d(Bare_point_d(p1.begin(), p1.end()), 0.)); - w_pts.push_back(Weighted_point_d(Bare_point_d(p2.begin(), p2.end()), 0.)); - w_pts.push_back(Weighted_point_d(Bare_point_d(p3.begin(), p3.end()), 0.)); - w_pts.push_back(Weighted_point_d(Bare_point_d(p4.begin(), p4.end()), 0.)); + w_pts.emplace_back(Bare_point_d(p0.begin(), p0.end()), 0.); + w_pts.emplace_back(Bare_point_d(p1.begin(), p1.end()), 0.); + w_pts.emplace_back(Bare_point_d(p2.begin(), p2.end()), 0.); + w_pts.emplace_back(Bare_point_d(p3.begin(), p3.end()), 0.); + w_pts.emplace_back(Bare_point_d(p4.begin(), p4.end()), 0.); Weighted_kernel w_kernel; auto w_sphere = w_kernel.get_sphere(w_pts.cbegin(), w_pts.cend()); diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index e86b34e2..3ce7b440 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -50,7 +50,7 @@ std::vector read_weight_file(const std::string &weight_file) { double weight = 0.0; // Attempt read the weight in a double format, return false if it fails while (weights_ifstr >> weight) { - weights.push_back(weight); + weights.emplace_back(weight); } } else { std::cerr << "Unable to read weights file " << weight_file << std::endl; -- cgit v1.2.3 From 74143b372d3d93fc2139974fa85906047acee8a7 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 10:33:23 +0200 Subject: code review: push_back versus emplace_back --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 6 +++--- src/Alpha_complex/utilities/alpha_complex_persistence.cpp | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 4f8e3d54..a692dbc6 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -310,7 +310,7 @@ class Alpha_complex { thread_local std::vector v; v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) - v.emplace_back(get_point_(vertex)); + v.push_back(get_point_(vertex)); cache_.emplace_back(kernel_.get_sphere(v.cbegin(), v.cend())); } return cache_[k]; @@ -326,7 +326,7 @@ class Alpha_complex { thread_local std::vector v; v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) - v.emplace_back(get_point_(vertex)); + v.push_back(get_point_(vertex)); return kernel_.get_squared_radius(v.cbegin(), v.cend()); } @@ -394,7 +394,7 @@ class Alpha_complex { std::clog << " " << (*vit)->data(); #endif // DEBUG_TRACES // Vector of vertex construction for simplex_tree structure - vertexVector.emplace_back((*vit)->data()); + vertexVector.push_back((*vit)->data()); } } #ifdef DEBUG_TRACES diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index 3ce7b440..e86b34e2 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -50,7 +50,7 @@ std::vector read_weight_file(const std::string &weight_file) { double weight = 0.0; // Attempt read the weight in a double format, return false if it fails while (weights_ifstr >> weight) { - weights.emplace_back(weight); + weights.push_back(weight); } } else { std::cerr << "Unable to read weights file " << weight_file << std::endl; -- cgit v1.2.3 From 7b477e78f38324bf1473966d59aab0360bae8066 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 10:38:31 +0200 Subject: code review: promote SAFE mode --- src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 09431d6e..ee12d418 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -7,9 +7,9 @@ #include #include // for numeric limits -// Complexity = FAST, weighted = true, periodic = false +// Complexity = SAFE, weighted = true, periodic = false using Weighted_alpha_complex_3d = - Gudhi::alpha_complex::Alpha_complex_3d; + Gudhi::alpha_complex::Alpha_complex_3d; using Bare_point = Weighted_alpha_complex_3d::Bare_point_3; using Weighted_point = Weighted_alpha_complex_3d::Weighted_point_3; -- cgit v1.2.3 From f0beb329f5a1767e4e0a0575ef3e078bf4563a44 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 11:12:44 +0200 Subject: code review: move test_wasserstein_distance_grad from test_wasserstein_distance.py to test_wasserstein_with_tensors.py --- src/python/CMakeLists.txt | 5 +++-- src/python/test/test_wasserstein_distance.py | 24 ---------------------- src/python/test/test_wasserstein_with_tensors.py | 26 ++++++++++++++++++++++-- 3 files changed, 27 insertions(+), 28 deletions(-) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index cc71503f..c09996fe 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -499,13 +499,14 @@ if(PYTHONINTERP_FOUND) # Wasserstein if(OT_FOUND AND PYBIND11_FOUND) - if(TORCH_FOUND AND EAGERPY_FOUND) + # EagerPy dependency because of enable_autodiff=True + if(EAGERPY_FOUND) add_gudhi_py_test(test_wasserstein_distance) endif() add_gudhi_py_test(test_wasserstein_barycenter) endif() if(OT_FOUND) - if(TENSORFLOW_FOUND AND EAGERPY_FOUND) + if(TORCH_FOUND AND TENSORFLOW_FOUND AND EAGERPY_FOUND) add_gudhi_py_test(test_wasserstein_with_tensors) endif() endif() diff --git a/src/python/test/test_wasserstein_distance.py b/src/python/test/test_wasserstein_distance.py index 90d26809..e3b521d6 100755 --- a/src/python/test/test_wasserstein_distance.py +++ b/src/python/test/test_wasserstein_distance.py @@ -97,27 +97,3 @@ def test_wasserstein_distance_pot(): def test_wasserstein_distance_hera(): _basic_wasserstein(hera_wrap(delta=1e-12), 1e-12, test_matching=False) _basic_wasserstein(hera_wrap(delta=.1), .1, test_matching=False) - -def test_wasserstein_distance_grad(): - import torch - - diag1 = torch.tensor([[2.7, 3.7], [9.6, 14.0], [34.2, 34.974]], requires_grad=True) - diag2 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True) - diag3 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True) - assert diag1.grad is None and diag2.grad is None and diag3.grad is None - dist12 = pot(diag1, diag2, internal_p=2, order=2, enable_autodiff=True) - dist30 = pot(diag3, torch.tensor([]), internal_p=2, order=2, enable_autodiff=True) - dist12.backward() - dist30.backward() - assert not torch.isnan(diag1.grad).any() and not torch.isnan(diag2.grad).any() and not torch.isnan(diag3.grad).any() - diag4 = torch.tensor([[0., 10.]], requires_grad=True) - diag5 = torch.tensor([[1., 11.], [3., 4.]], requires_grad=True) - dist45 = pot(diag4, diag5, internal_p=1, order=1, enable_autodiff=True) - assert dist45 == 3. - dist45.backward() - assert np.array_equal(diag4.grad, [[-1., -1.]]) - assert np.array_equal(diag5.grad, [[1., 1.], [-1., 1.]]) - diag6 = torch.tensor([[5., 10.]], requires_grad=True) - pot(diag6, diag6, internal_p=2, order=2, enable_autodiff=True).backward() - # https://github.com/jonasrauber/eagerpy/issues/6 - # assert np.array_equal(diag6.grad, [[0., 0.]]) diff --git a/src/python/test/test_wasserstein_with_tensors.py b/src/python/test/test_wasserstein_with_tensors.py index 8957705d..e3f1411a 100755 --- a/src/python/test/test_wasserstein_with_tensors.py +++ b/src/python/test/test_wasserstein_with_tensors.py @@ -10,10 +10,32 @@ from gudhi.wasserstein import wasserstein_distance as pot import numpy as np +import torch +import tensorflow as tf -def test_wasserstein_distance_grad_tensorflow(): - import tensorflow as tf +def test_wasserstein_distance_grad(): + diag1 = torch.tensor([[2.7, 3.7], [9.6, 14.0], [34.2, 34.974]], requires_grad=True) + diag2 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True) + diag3 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True) + assert diag1.grad is None and diag2.grad is None and diag3.grad is None + dist12 = pot(diag1, diag2, internal_p=2, order=2, enable_autodiff=True) + dist30 = pot(diag3, torch.tensor([]), internal_p=2, order=2, enable_autodiff=True) + dist12.backward() + dist30.backward() + assert not torch.isnan(diag1.grad).any() and not torch.isnan(diag2.grad).any() and not torch.isnan(diag3.grad).any() + diag4 = torch.tensor([[0., 10.]], requires_grad=True) + diag5 = torch.tensor([[1., 11.], [3., 4.]], requires_grad=True) + dist45 = pot(diag4, diag5, internal_p=1, order=1, enable_autodiff=True) + assert dist45 == 3. + dist45.backward() + assert np.array_equal(diag4.grad, [[-1., -1.]]) + assert np.array_equal(diag5.grad, [[1., 1.], [-1., 1.]]) + diag6 = torch.tensor([[5., 10.]], requires_grad=True) + pot(diag6, diag6, internal_p=2, order=2, enable_autodiff=True).backward() + # https://github.com/jonasrauber/eagerpy/issues/6 + # assert np.array_equal(diag6.grad, [[0., 0.]]) +def test_wasserstein_distance_grad_tensorflow(): with tf.GradientTape() as tape: diag4 = tf.convert_to_tensor(tf.Variable(initial_value=np.array([[0., 10.]]), trainable=True)) diag5 = tf.convert_to_tensor(tf.Variable(initial_value=np.array([[1., 11.], [3., 4.]]), trainable=True)) -- cgit v1.2.3 From 3b839cae75a7e58b87216ee92356267bbe873e46 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 11:26:24 +0200 Subject: doc review: eigen 3.3.5 and cgal 5.2.0 is advised for perf reasons not only on weighted version --- src/Alpha_complex/doc/Intro_alpha_complex.h | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 78486ad6..fb051760 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -74,7 +74,7 @@ Table of Contents * [10^12,10^12+10^6]. Using `CGAL::Epick_d` makes the computations slightly faster, and the combinatorics are still * exact, but the computation of filtration values can exceptionally be arbitrarily bad. In all cases, we still * guarantee that the output is a valid filtration (faces have a filtration value no larger than their cofaces). - * - For performances reasons, it is advised to use `Alpha_complex` with \ref cgal ≥ 5.0.0. + * - For performances reasons, it is advised to use \ref eigen ≥ 3.3.5 and \ref cgal ≥ 5.2.0. * * \section pointsexample Example from points * @@ -160,7 +160,6 @@ Table of Contents * * \section weightedversion Weighted specific version * Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 5.1.0. - * For performances reasons, it is advised to use \ref eigen ≥ 3.3.5 and \ref cgal ≥ 5.2.0. * * A weighted version for Alpha complex is available (cf. Alpha_complex). * -- cgit v1.2.3 From 9bba01c0afb2c931553d2c47af0104f407d22c01 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 13:18:59 +0200 Subject: code review: typename is useless here --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index a692dbc6..ae04e6e8 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -134,7 +134,7 @@ class Alpha_complex { using size_type = typename Triangulation::size_type; // Structure to switch from simplex tree vertex handle to CGAL vertex iterator. - using Vector_vertex_iterator = typename std::vector< CGAL_vertex_iterator >; + using Vector_vertex_iterator = std::vector< CGAL_vertex_iterator >; private: /** \brief Vertex iterator vector to switch from simplex tree vertex handle to CGAL vertex iterator. -- cgit v1.2.3 From f7faba86fced9c75c530c86665ca3c73429d8f12 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 13:19:52 +0200 Subject: code review: include what you use --- src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index a6760645..7c49bb14 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -11,8 +11,6 @@ #ifndef ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ #define ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ -#include // For EXACT or SAFE version -#include // For FAST version #include // for CGAL_VERSION_NR #include // for EIGEN_VERSION_AT_LEAST -- cgit v1.2.3 From 2d80f0e7f3e09167760338c15596b052050ddb55 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 14:00:51 +0200 Subject: code review: roll back include epick --- src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index 7c49bb14..d4dbd68b 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -12,6 +12,8 @@ #define ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ #include // for CGAL_VERSION_NR +#include // For EXACT or SAFE version +#include // For FAST version #include // for EIGEN_VERSION_AT_LEAST -- cgit v1.2.3 From d6ca67fee4f9c2a97b64710a5b70ed66dd307372 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 14:50:57 +0200 Subject: code review: fix include what you use and compute_squared_radius_smallest_orthogonal_sphere_d_object use --- src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index d4dbd68b..fbb931d4 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -12,10 +12,8 @@ #define ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ #include // for CGAL_VERSION_NR -#include // For EXACT or SAFE version -#include // For FAST version -#include // for EIGEN_VERSION_AT_LEAST +#include // for EIGEN_VERSION_AT_LEAST #include // for std::make_pair @@ -117,7 +115,7 @@ class Alpha_kernel_d { template FT get_squared_radius(PointIterator begin, PointIterator end) const { - return get_sphere(begin, end).weight(); + return kernel_.compute_squared_radius_smallest_orthogonal_sphere_d_object()(begin, end); } FT get_squared_radius(const Sphere& sph) const { -- cgit v1.2.3 From 298925b9c2dc3629f2d20ad9b85f5a410dee6fab Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 15:29:25 +0200 Subject: code review: use geom_trait for Point_d type --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index ae04e6e8..1963f02b 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -124,7 +124,7 @@ class Alpha_complex { using Sphere = typename A_kernel_d::Sphere; /** \brief A point, or a weighted point in Euclidean space.*/ - using Point_d = std::conditional_t; + using Point_d = typename Geom_traits::Point_d; private: // Vertex_iterator type from CGAL. -- cgit v1.2.3 From 51f4de9a42cbdf7686a0f36106b31c0d3296ccfa Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 5 Oct 2020 16:11:46 +0200 Subject: doc review: Add some precision about regular triangulations --- src/Alpha_complex/doc/Intro_alpha_complex.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index fb051760..c068b268 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -161,7 +161,9 @@ Table of Contents * \section weightedversion Weighted specific version * Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 5.1.0. * - * A weighted version for Alpha complex is available (cf. Alpha_complex). + * A weighted version for Alpha complex is available (cf. Alpha_complex). It is like a usual Alpha complex, but based + * on a CGAL regular triangulation instead + * of Delaunay. * * This example builds the CGAL weighted alpha shapes from a small molecule, and initializes the alpha complex with * it. This example is taken from CGAL 3d -- cgit v1.2.3 From 30efe05d095051e14cbaf26d12fc2a67134e5a60 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 15 Oct 2020 16:43:54 +0200 Subject: Use unique_ptr for triangulation_ --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 1963f02b..4f7a7bd2 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -19,6 +19,7 @@ #include #include // isnan, fmax +#include // for std::unique_ptr #include #include // aka. Weighted Delaunay triangulation @@ -141,7 +142,7 @@ class Alpha_complex { * Vertex handles are inserted sequentially, starting at 0.*/ Vector_vertex_iterator vertex_handle_to_iterator_; /** \brief Pointer on the CGAL Delaunay triangulation.*/ - Triangulation* triangulation_; + std::unique_ptr triangulation_; /** \brief Kernel for triangulation_ functions access.*/ A_kernel_d kernel_; @@ -158,8 +159,7 @@ class Alpha_complex { * * @param[in] off_file_name OFF file [path and] name. */ - Alpha_complex(const std::string& off_file_name) - : triangulation_(nullptr) { + Alpha_complex(const std::string& off_file_name) { Gudhi::Points_off_reader off_reader(off_file_name); if (!off_reader.is_valid()) { std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n"; @@ -180,8 +180,7 @@ class Alpha_complex { * Kernel::Point_d or Kernel::Weighted_point_d. */ template - Alpha_complex(const InputPointRange& points) - : triangulation_(nullptr) { + Alpha_complex(const InputPointRange& points) { init_from_range(points); } @@ -208,12 +207,6 @@ class Alpha_complex { init_from_range(weighted_points); } - /** \brief Alpha_complex destructor deletes the Delaunay triangulation. - */ - ~Alpha_complex() { - delete triangulation_; - } - // Forbid copy/move constructor/assignment operator Alpha_complex(const Alpha_complex& other) = delete; Alpha_complex& operator= (const Alpha_complex& other) = delete; @@ -249,7 +242,7 @@ class Alpha_complex { if (first != last) { // Delaunay triangulation init with point dimension. - triangulation_ = new Triangulation(kernel_.get_dimension(*first)); + triangulation_ = std::make_unique(kernel_.get_dimension(*first)); std::vector point_cloud(first, last); -- cgit v1.2.3 From 7f2eefc474cb32dc5d566c5c370b03478c1996ac Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sat, 17 Oct 2020 19:14:09 +0200 Subject: Replace diameter (actually max y) with max distance to diagonal --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 2 +- .../include/gudhi/Persistence_graph.h | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index e466828a..ad437710 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -35,7 +35,7 @@ namespace persistence_diagram { inline double bottleneck_distance_approx(Persistence_graph& g, double e) { double b_lower_bound = 0.; - double b_upper_bound = g.diameter_bound(); + double b_upper_bound = g.max_dist_to_diagonal(); const double alpha = std::pow(g.size(), 1. / 5.); Graph_matching m(g); Graph_matching biggest_unperfect(g); diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index e1e3522e..04c7c118 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -51,8 +51,8 @@ class Persistence_graph { double bottleneck_alive() const; /** \internal \brief Returns the O(n^2) sorted distances between the points. */ std::vector sorted_distances() const; - /** \internal \brief Returns an upper bound for the diameter of the convex hull of all non infinite points */ - double diameter_bound() const; + /** \internal \brief Returns an upper bound for the bottleneck distance of the finite points. */ + double max_dist_to_diagonal() const; /** \internal \brief Returns the corresponding internal point */ Internal_point get_u_point(int u_point_index) const; /** \internal \brief Returns the corresponding internal point */ @@ -160,13 +160,13 @@ inline Internal_point Persistence_graph::get_v_point(int v_point_index) const { return Internal_point(m, m, v_point_index); } -inline double Persistence_graph::diameter_bound() const { +inline double Persistence_graph::max_dist_to_diagonal() const { double max = 0.; - for (auto it = u.cbegin(); it != u.cend(); it++) - max = (std::max)(max, it->y()); - for (auto it = v.cbegin(); it != v.cend(); it++) - max = (std::max)(max, it->y()); - return max; + for (auto& p : u) + max = (std::max)(max, p.y() - p.x()); + for (auto& p : v) + max = (std::max)(max, p.y() - p.x()); + return max / 2; } } // namespace persistence_diagram -- cgit v1.2.3 From 27a488386c6a3b2b4dbac43534a36f18ef04ac80 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sat, 17 Oct 2020 19:15:58 +0200 Subject: Don't put a (useless) point on the diagonal in the example --- src/python/doc/bottleneck_distance_user.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/python/doc/bottleneck_distance_user.rst b/src/python/doc/bottleneck_distance_user.rst index 6c6e08d9..418dd11f 100644 --- a/src/python/doc/bottleneck_distance_user.rst +++ b/src/python/doc/bottleneck_distance_user.rst @@ -35,19 +35,19 @@ The following example explains how the distance is computed: import gudhi - message = "Bottleneck distance = " + '%.1f' % gudhi.bottleneck_distance([[0., 0.]], [[0., 13.]]) + message = "Bottleneck distance = " + '%.1f' % gudhi.bottleneck_distance([[0., 2.]], [[1., 13.]]) print(message) .. testoutput:: - Bottleneck distance = 6.5 + Bottleneck distance = 6.0 .. figure:: ../../doc/Bottleneck_distance/bottleneck_distance_example.png :figclass: align-center - The point (0, 13) is at distance 6.5 from the diagonal and more - specifically from the point (6.5, 6.5) + The point (1, 13) is at distance 6 from the diagonal and more + specifically from the point (7, 7). Basic example -- cgit v1.2.3 From 911b589081831c98040448c489264fabfe8b5558 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sat, 17 Oct 2020 23:29:39 +0200 Subject: Handle diagrams with a single point --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 6 +++++- src/Bottleneck_distance/include/gudhi/Persistence_graph.h | 2 +- src/Bottleneck_distance/test/bottleneck_unit_test.cpp | 5 +++++ src/python/doc/bottleneck_distance_user.rst | 2 +- 4 files changed, 12 insertions(+), 3 deletions(-) diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index ad437710..c916898d 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -36,7 +36,11 @@ namespace persistence_diagram { inline double bottleneck_distance_approx(Persistence_graph& g, double e) { double b_lower_bound = 0.; double b_upper_bound = g.max_dist_to_diagonal(); - const double alpha = std::pow(g.size(), 1. / 5.); + int siz = g.size(); + if (siz <= 1) + // The value of alpha would be wrong in this case + return b_upper_bound; + const double alpha = std::pow(siz, 1. / 5.); Graph_matching m(g); Graph_matching biggest_unperfect(g); while (b_upper_bound - b_lower_bound > 2 * e) { diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index 04c7c118..33f03b9c 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -45,7 +45,7 @@ class Persistence_graph { int corresponding_point_in_v(int u_point_index) const; /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ double distance(int u_point_index, int v_point_index) const; - /** \internal \brief Returns size = |U| = |V|. */ + /** \internal \brief Returns size = |U| + |V|. */ int size() const; /** \internal \brief Is there as many infinite points (alive components) in both diagrams ? */ double bottleneck_alive() const; diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index 2c520045..44141baa 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -153,4 +153,9 @@ BOOST_AUTO_TEST_CASE(global) { BOOST_CHECK(bottleneck_distance(v1, v2, 0.) <= upper_bound / 100.); BOOST_CHECK(bottleneck_distance(v1, v2, upper_bound / 10000.) <= upper_bound / 100. + upper_bound / 10000.); BOOST_CHECK(std::abs(bottleneck_distance(v1, v2, 0.) - bottleneck_distance(v1, v2, upper_bound / 10000.)) <= upper_bound / 10000.); + + std::vector< std::pair > empty; + std::vector< std::pair > one = {{8, 10}}; + BOOST_CHECK(bottleneck_distance(empty, empty) == 0); + BOOST_CHECK(bottleneck_distance(empty, one) == 1); } diff --git a/src/python/doc/bottleneck_distance_user.rst b/src/python/doc/bottleneck_distance_user.rst index 418dd11f..2c74c6dd 100644 --- a/src/python/doc/bottleneck_distance_user.rst +++ b/src/python/doc/bottleneck_distance_user.rst @@ -72,6 +72,6 @@ The output is: .. testoutput:: - Bottleneck distance approximation = 0.81 + Bottleneck distance approximation = 0.72 Bottleneck distance value = 0.75 -- cgit v1.2.3 From c66b9126429e1ff18f9ca69b27c5f357f071a697 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Mon, 19 Oct 2020 01:05:04 +0200 Subject: Handle duplicated points --- src/Subsampling/include/gudhi/choose_n_farthest_points.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index 66421a69..38c3a76b 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -111,6 +111,8 @@ void choose_n_farthest_points(Kernel const &k, curr_max_dist = dist_to_L[i]; curr_max_w = i; } + // If all that remains are duplicates of points already taken, stop. + if (curr_max_dist == 0) break; } } -- 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(-) 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 From 8aea376ed0b3c9066fb7e649f1cd66ffbed99a8d Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Thu, 22 Oct 2020 22:27:10 +0200 Subject: Simplify strange iterator use the syntax with [] is already used a few lines above --- src/Subsampling/include/gudhi/choose_n_farthest_points.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index 0e13fc5a..b70af8a0 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -100,7 +100,7 @@ void choose_n_farthest_points(Kernel const &k, *dist_it++ = dist_to_L[curr_max_w]; std::size_t i = 0; for (auto&& p : input_pts) { - double curr_dist = sqdist(p, *(std::begin(input_pts) + curr_max_w)); + double curr_dist = sqdist(p, input_pts[curr_max_w]); if (curr_dist < dist_to_L[i]) dist_to_L[i] = curr_dist; ++i; -- cgit v1.2.3 From 3ae0bc89f6ef853c1c52fc609bfe08097d3594db Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Thu, 22 Oct 2020 22:49:23 +0200 Subject: test with duplicated point --- src/Subsampling/test/test_choose_n_farthest_points.cpp | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/src/Subsampling/test/test_choose_n_farthest_points.cpp b/src/Subsampling/test/test_choose_n_farthest_points.cpp index 5c4bd4cb..08b82d61 100644 --- a/src/Subsampling/test/test_choose_n_farthest_points.cpp +++ b/src/Subsampling/test/test_choose_n_farthest_points.cpp @@ -93,7 +93,15 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of std::vector point2({1.0, 0.0, 0.0, 0.0}); points.push_back(Point_d(point2.begin(), point2.end())); - // Choose all farthest points in a one point cloud + // Choose all farthest points among 2 points + Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + BOOST_CHECK(landmarks.size() == 2 && distances.size() == 2); + BOOST_CHECK(distances[0] == std::numeric_limits::infinity()); + BOOST_CHECK(distances[1] == 1); + landmarks.clear(); distances.clear(); + + // Ignore duplicated points + points.push_back(Point_d(point.begin(), point.end())); Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 2 && distances.size() == 2); BOOST_CHECK(distances[0] == std::numeric_limits::infinity()); -- cgit v1.2.3 From afafd56fdb4a53b66ca3354fc20f787f12340fa4 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 26 Oct 2020 10:56:25 +0100 Subject: for CGAL 5.2 pre-release to work --- src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index fbb931d4..28d6d7a9 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -106,7 +106,7 @@ class Alpha_kernel_d { template Sphere get_sphere(PointIterator begin, PointIterator end) const { // power_center_d_object has been renamed between CGAL 5.1 and 5.2 -#if CGAL_VERSION_NR < 1050201000 +#if CGAL_VERSION_NR < 1050200000 return kernel_.power_center_d_object()(begin, end); #else return kernel_.construct_power_sphere_d_object()(begin, end); @@ -124,7 +124,7 @@ class Alpha_kernel_d { bool is_gabriel(const Sphere& circumcenter, const Weighted_point_d& point) { // power_center_d_object has been renamed between CGAL 5.1 and 5.2 -#if CGAL_VERSION_NR < 1050201000 +#if CGAL_VERSION_NR < 1050200000 return kernel_.power_distance_d_object()(circumcenter, point) >= 0; #else return kernel_.compute_power_product_d_object()(circumcenter, point) >= 0; -- cgit v1.2.3 From 699a89819da922222cedcd81b4a1553ee161a633 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 26 Oct 2020 10:58:19 +0100 Subject: code review: bad copy/paste that needs rephrase --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 4f7a7bd2..b315fa99 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -198,7 +198,7 @@ class Alpha_complex { */ template Alpha_complex(const InputPointRange& points, WeightRange weights) { - static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d"); + static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex"); // FIXME: this test is only valid if we have a forward range GUDHI_CHECK(boost::size(weights) == boost::size(points), std::invalid_argument("Points number in range different from weights range number")); -- cgit v1.2.3 From 4d8c5c315b79260fbae05d359987c8d39a863d2d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 27 Oct 2020 11:15:36 +0100 Subject: zero weighted test is guaranteed only for exact version --- src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index e8372656..cae9dbb5 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -29,14 +29,10 @@ // Use dynamic_dimension_tag for the user to be able to set dimension typedef CGAL::Epeck_d< CGAL::Dynamic_dimension_tag > Exact_kernel_d; -// Use static dimension_tag for the user not to be able to set dimension +// Use static dimension_tag to set dimension at 4 typedef CGAL::Epeck_d< CGAL::Dimension_tag<4> > Exact_kernel_s; -// Use dynamic_dimension_tag for the user to be able to set dimension -typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Inexact_kernel_d; -// Use static dimension_tag for the user not to be able to set dimension -typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Inexact_kernel_s; -typedef boost::mpl::list list_of_kernel_variants; +typedef boost::mpl::list list_of_kernel_variants; BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_kernel_variants) { // Random points construction @@ -53,7 +49,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_kerne // Alpha complex from points Gudhi::alpha_complex::Alpha_complex alpha_complex_from_points(points); Gudhi::Simplex_tree<> simplex; - BOOST_CHECK(alpha_complex_from_points.create_complex(simplex)); + BOOST_CHECK(alpha_complex_from_points.create_complex(simplex, std::numeric_limits::Filtration_value>::infinity(), true)); std::clog << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : simplex.filtration_simplex_range()) { std::clog << " ( "; @@ -68,7 +64,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_kerne std::vector weights(20, 0.); Gudhi::alpha_complex::Alpha_complex alpha_complex_from_zero_weighted_points(points, weights); Gudhi::Simplex_tree<> zw_simplex; - BOOST_CHECK(alpha_complex_from_zero_weighted_points.create_complex(zw_simplex)); + BOOST_CHECK(alpha_complex_from_zero_weighted_points.create_complex(zw_simplex, std::numeric_limits::Filtration_value>::infinity(), true)); std::clog << "Iterator on zero weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : zw_simplex.filtration_simplex_range()) { -- cgit v1.2.3 From beaa5c2fa89ed92c84328383ac58f1e71cf510ff Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 27 Oct 2020 12:16:34 +0100 Subject: Add a test for non visible points (hidden by weights) --- .../test/Weighted_alpha_complex_unit_test.cpp | 35 ++++++++++++++++++++-- 1 file changed, 32 insertions(+), 3 deletions(-) diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index cae9dbb5..cc63ac1f 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -43,7 +43,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_kerne std::mt19937 rand_engine(rand_dev()); for (int idx = 0; idx < 20; idx++) { std::vector point {rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine)}; - points.emplace_back(Point_d(point.begin(), point.end())); + points.emplace_back(point.begin(), point.end()); } // Alpha complex from points @@ -108,8 +108,8 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { for (int idx = 0; idx < 20; idx++) { std::vector point {rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine)}; double weight = rd_wghts(rand_engine); - w_points_d.emplace_back(Weighted_point_d(Bare_point_d(point.begin(), point.end()), weight)); - w_points_3.emplace_back(Weighted_point_3(Bare_point_3(point[0], point[1], point[2]), weight)); + w_points_d.emplace_back(Bare_point_d(point.begin(), point.end()), weight); + w_points_3.emplace_back(Bare_point_3(point[0], point[1], point[2]), weight); } // Structures necessary for comparison @@ -185,3 +185,32 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { ++dD_itr; } } + +BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_non_visible_points) { + using Point_d = typename Exact_kernel_d::Point_d; + std::vector points; + std::vector p1 {0.}; + points.emplace_back(p1.begin(), p1.end()); + // closed enough points + std::vector p2 {0.1}; + points.emplace_back(p2.begin(), p2.end()); + std::vector weights {100., 0.01}; + + Gudhi::alpha_complex::Alpha_complex alpha_complex(points, weights); + Gudhi::Simplex_tree<> stree; + BOOST_CHECK(alpha_complex.create_complex(stree)); + + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << stree.filtration(f_simplex) << "] "; + std::clog << std::endl; + } + + BOOST_CHECK(stree.filtration(stree.find({0})) == -100.); + BOOST_CHECK(stree.filtration(stree.find({1})) == stree.filtration(stree.find({0, 1}))); + +} \ No newline at end of file -- cgit v1.2.3 From 901fbd0ccdee2d9bb7794de8896d35aae8ede989 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 27 Oct 2020 14:45:25 +0100 Subject: Add a test about the filtration --- src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index cc63ac1f..b84ab3de 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -212,5 +212,6 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_non_visible_points) { BOOST_CHECK(stree.filtration(stree.find({0})) == -100.); BOOST_CHECK(stree.filtration(stree.find({1})) == stree.filtration(stree.find({0, 1}))); + BOOST_CHECK(stree.filtration(stree.find({1})) > 100000); } \ No newline at end of file -- cgit v1.2.3 From 705aa3b7ddc0a2bbbcc31c4b45e19792bd4ce9a5 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Wed, 28 Oct 2020 00:04:37 +0100 Subject: emplace_back --- src/Subsampling/test/test_choose_n_farthest_points.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/Subsampling/test/test_choose_n_farthest_points.cpp b/src/Subsampling/test/test_choose_n_farthest_points.cpp index 08b82d61..b318d58e 100644 --- a/src/Subsampling/test/test_choose_n_farthest_points.cpp +++ b/src/Subsampling/test/test_choose_n_farthest_points.cpp @@ -39,7 +39,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point, Kernel, list_of_tested for (FT k = 0; k < 5; k += 1.0) for (FT l = 0; l < 5; l += 1.0) { std::vector point({i, j, k, l}); - points.push_back(Point_d(point.begin(), point.end())); + points.emplace_back(point.begin(), point.end()); } landmarks.clear(); @@ -75,7 +75,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of landmarks.clear(); distances.clear(); std::vector point({0.0, 0.0, 0.0, 0.0}); - points.push_back(Point_d(point.begin(), point.end())); + points.emplace_back(point.begin(), point.end()); // Choose -1 farthest points in a one point cloud Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 1 && distances.size() == 1); @@ -92,7 +92,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of landmarks.clear(); distances.clear(); std::vector point2({1.0, 0.0, 0.0, 0.0}); - points.push_back(Point_d(point2.begin(), point2.end())); + points.emplace_back(point2.begin(), point2.end()); // Choose all farthest points among 2 points Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 2 && distances.size() == 2); @@ -101,7 +101,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of landmarks.clear(); distances.clear(); // Ignore duplicated points - points.push_back(Point_d(point.begin(), point.end())); + points.emplace_back(point.begin(), point.end()); Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 2 && distances.size() == 2); BOOST_CHECK(distances[0] == std::numeric_limits::infinity()); -- cgit v1.2.3 From 666f3f54498f47f1bc1cddbd522e5f53b9aae63a Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 3 Nov 2020 09:27:21 +0100 Subject: Add comment in code for get_boundaries if not interested in filtration values --- src/python/gudhi/simplex_tree.pyx | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index c671da56..813dc5c2 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -287,6 +287,8 @@ cdef class SimplexTree: def get_boundaries(self, simplex): """This function returns a generator with the boundaries of a given N-simplex. + If you do not need the filtration values, the boundary can also be obtained as + :code:`itertools.combinations(simplex,len(simplex)-1)`. :param simplex: The N-simplex, represented by a list of vertex. :type simplex: list of int. -- cgit v1.2.3 From 69c70afd0442774582b7e930bdab603600a3e750 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 3 Nov 2020 11:33:39 +0100 Subject: doc review: explain briefly test aims --- .../test/Alpha_kernel_d_unit_test.cpp | 5 ++++ .../test/Weighted_alpha_complex_unit_test.cpp | 30 ++++++++++++++-------- 2 files changed, 25 insertions(+), 10 deletions(-) diff --git a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp index 6eae103d..6da4c084 100644 --- a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp @@ -37,6 +37,8 @@ typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Inexact_kernel_s; typedef boost::mpl::list list_of_kernel_variants; BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_dimension, TestedKernel, list_of_kernel_variants) { + // Test for a point (weighted or not) in 4d, that the dimension is 4. + Gudhi::alpha_complex::Alpha_kernel_d kernel; std::vector p0 {0., 1., 2., 3.}; typename TestedKernel::Point_d p0_d(p0.begin(), p0.end()); @@ -52,6 +54,9 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_dimension, TestedKernel, list_of_ke } BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_sphere, TestedKernel, list_of_kernel_variants) { + // Test with 5 points on a 3-sphere, that get_sphere returns the same center and squared radius + // for dD unweighted and for dD weighted with all weights at 0. + using Unweighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d; // Sphere: (x-1)² + (y-1)² + z² + t² = 1 // At least 5 points for a 3-sphere diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index b84ab3de..2cd66963 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -27,14 +27,14 @@ #include #include -// Use dynamic_dimension_tag for the user to be able to set dimension -typedef CGAL::Epeck_d< CGAL::Dynamic_dimension_tag > Exact_kernel_d; -// Use static dimension_tag to set dimension at 4 -typedef CGAL::Epeck_d< CGAL::Dimension_tag<4> > Exact_kernel_s; +using list_of_exact_kernel_variants = boost::mpl::list, + CGAL::Epeck_d< CGAL::Dimension_tag<4> > + > ; -typedef boost::mpl::list list_of_kernel_variants; +BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_exact_kernel_variants) { + // Check that in exact mode for static dimension 4 the code for dD unweighted and for dD weighted with all weights + // 0 give exactly the same simplex tree (simplices and filtration values). -BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_kernel_variants) { // Random points construction using Point_d = typename Kernel::Point_d; std::vector points; @@ -89,6 +89,8 @@ bool cgal_3d_point_sort (Point_d a,Point_d b) { } BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { + // check that for random weighted 3d points in safe mode the 3D and dD codes give the same result with some tolerance + // Random points construction using Kernel_dD = CGAL::Epeck_d< CGAL::Dimension_tag<3> >; using Bare_point_d = typename Kernel_dD::Point_d; @@ -186,17 +188,25 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { } } -BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_non_visible_points) { - using Point_d = typename Exact_kernel_d::Point_d; +using list_of_1d_kernel_variants = boost::mpl::list, + CGAL::Epeck_d< CGAL::Dimension_tag<1>>, + CGAL::Epick_d< CGAL::Dynamic_dimension_tag >, + CGAL::Epick_d< CGAL::Dimension_tag<1>> + >; + +BOOST_AUTO_TEST_CASE_TEMPLATE(Weighted_alpha_complex_non_visible_points, Kernel, list_of_1d_kernel_variants) { + // check that for 2 closed weighted 1-d points, one with a high weight to hide the second one with a small weight, + // that the point with a small weight has the same high filtration value than the edge formed by the 2 points + using Point_d = typename Kernel::Point_d; std::vector points; std::vector p1 {0.}; points.emplace_back(p1.begin(), p1.end()); // closed enough points std::vector p2 {0.1}; points.emplace_back(p2.begin(), p2.end()); - std::vector weights {100., 0.01}; + std::vector weights {100., 0.01}; - Gudhi::alpha_complex::Alpha_complex alpha_complex(points, weights); + Gudhi::alpha_complex::Alpha_complex alpha_complex(points, weights); Gudhi::Simplex_tree<> stree; BOOST_CHECK(alpha_complex.create_complex(stree)); -- cgit v1.2.3 From baaf350869dbd5ff78e22cc4c3de9b8ab35b75ba Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 3 Nov 2020 11:56:52 +0100 Subject: code review: use relative error --- src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index 2cd66963..3df76dbf 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -179,8 +179,8 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { std::clog << std::endl; BOOST_CHECK(false); } - // I had to make a hard limit as it is converted from Kernel::FT - if (std::fabs(d3_itr->second - dD_itr->second) > 1e-5) { + // In safe mode, relative error is less than 1e-5 (can be changed with set_relative_precision_of_to_double) + if (std::fabs(d3_itr->second - dD_itr->second) / std::fabs(d3_itr->second) > 1e-5) { std::clog << d3_itr->second << " versus " << dD_itr->second << " diff " << std::fabs(d3_itr->second - dD_itr->second) << std::endl; BOOST_CHECK(false); } -- cgit v1.2.3 From 05e28e39717c4ca5871b13a350c4b142ec9a173b Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 3 Nov 2020 14:09:05 +0100 Subject: code review: use Marc's trick to test relative error --- .../test/Weighted_alpha_complex_unit_test.cpp | 38 ++++++++++++---------- 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp index 3df76dbf..d267276c 100644 --- a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -49,31 +49,32 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_exact // Alpha complex from points Gudhi::alpha_complex::Alpha_complex alpha_complex_from_points(points); Gudhi::Simplex_tree<> simplex; - BOOST_CHECK(alpha_complex_from_points.create_complex(simplex, std::numeric_limits::Filtration_value>::infinity(), true)); - std::clog << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + Gudhi::Simplex_tree<>::Filtration_value infty = std::numeric_limits::Filtration_value>::infinity(); + BOOST_CHECK(alpha_complex_from_points.create_complex(simplex, infty, true)); + std::clog << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" + << std::endl; for (auto f_simplex : simplex.filtration_simplex_range()) { std::clog << " ( "; for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { std::clog << vertex << " "; } - std::clog << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; - std::clog << std::endl; + std::clog << ") -> " << "[" << simplex.filtration(f_simplex) << "] " << std::endl; } // Alpha complex from zero weighted points std::vector weights(20, 0.); Gudhi::alpha_complex::Alpha_complex alpha_complex_from_zero_weighted_points(points, weights); Gudhi::Simplex_tree<> zw_simplex; - BOOST_CHECK(alpha_complex_from_zero_weighted_points.create_complex(zw_simplex, std::numeric_limits::Filtration_value>::infinity(), true)); + BOOST_CHECK(alpha_complex_from_zero_weighted_points.create_complex(zw_simplex, infty, true)); - std::clog << "Iterator on zero weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + std::clog << "Iterator on zero weighted alpha complex simplices in the filtration order, with [filtration value]:" + << std::endl; for (auto f_simplex : zw_simplex.filtration_simplex_range()) { std::clog << " ( "; for (auto vertex : zw_simplex.simplex_vertex_range(f_simplex)) { std::clog << vertex << " "; } - std::clog << ") -> " << "[" << zw_simplex.filtration(f_simplex) << "] "; - std::clog << std::endl; + std::clog << ") -> " << "[" << zw_simplex.filtration(f_simplex) << "] " << std::endl; } BOOST_CHECK(zw_simplex == simplex); @@ -125,7 +126,8 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { Gudhi::Simplex_tree<> w_simplex_d; BOOST_CHECK(alpha_complex_dD_from_weighted_points.create_complex(w_simplex_d)); - std::clog << "Iterator on weighted alpha complex dD simplices in the filtration order, with [filtration value]:" << std::endl; + std::clog << "Iterator on weighted alpha complex dD simplices in the filtration order, with [filtration value]:" + << std::endl; for (auto f_simplex : w_simplex_d.filtration_simplex_range()) { Points points; for (auto vertex : w_simplex_d.simplex_vertex_range(f_simplex)) { @@ -148,7 +150,8 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { Gudhi::Simplex_tree<> w_simplex_3; BOOST_CHECK(alpha_complex_3D_from_weighted_points.create_complex(w_simplex_3)); - std::clog << "Iterator on weighted alpha complex 3D simplices in the filtration order, with [filtration value]:" << std::endl; + std::clog << "Iterator on weighted alpha complex 3D simplices in the filtration order, with [filtration value]:" + << std::endl; for (auto f_simplex : w_simplex_3.filtration_simplex_range()) { Points points; for (auto vertex : w_simplex_3.simplex_vertex_range(f_simplex)) { @@ -161,8 +164,7 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { for (auto point : points) { std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; } - std::clog << ") -> " << "[" << w_simplex_3.filtration(f_simplex) << "] "; - std::clog << std::endl; + std::clog << ") -> " << "[" << w_simplex_3.filtration(f_simplex) << "] " << std::endl; pts_fltr_3d[points] = w_simplex_d.filtration(f_simplex); } @@ -180,8 +182,9 @@ BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { BOOST_CHECK(false); } // In safe mode, relative error is less than 1e-5 (can be changed with set_relative_precision_of_to_double) - if (std::fabs(d3_itr->second - dD_itr->second) / std::fabs(d3_itr->second) > 1e-5) { - std::clog << d3_itr->second << " versus " << dD_itr->second << " diff " << std::fabs(d3_itr->second - dD_itr->second) << std::endl; + if (std::fabs(d3_itr->second - dD_itr->second) > 1e-5 * (std::fabs(d3_itr->second) + std::fabs(dD_itr->second))) { + std::clog << d3_itr->second << " versus " << dD_itr->second << " diff " + << std::fabs(d3_itr->second - dD_itr->second) << std::endl; BOOST_CHECK(false); } ++dD_itr; @@ -210,18 +213,17 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Weighted_alpha_complex_non_visible_points, Kernel, Gudhi::Simplex_tree<> stree; BOOST_CHECK(alpha_complex.create_complex(stree)); - std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" + << std::endl; for (auto f_simplex : stree.filtration_simplex_range()) { std::clog << " ( "; for (auto vertex : stree.simplex_vertex_range(f_simplex)) { std::clog << vertex << " "; } - std::clog << ") -> " << "[" << stree.filtration(f_simplex) << "] "; - std::clog << std::endl; + std::clog << ") -> " << "[" << stree.filtration(f_simplex) << "] " << std::endl; } BOOST_CHECK(stree.filtration(stree.find({0})) == -100.); BOOST_CHECK(stree.filtration(stree.find({1})) == stree.filtration(stree.find({0, 1}))); BOOST_CHECK(stree.filtration(stree.find({1})) > 100000); - } \ No newline at end of file -- cgit v1.2.3 From 2d4c69d698df7e40709ec0e38463b4cf30ee388d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 3 Nov 2020 17:39:07 +0100 Subject: Fix #416 by adding full path to introduction.rst - maybe strange with conda or pip installation --- src/python/setup.py.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 98d058fc..1d6745fd 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -65,7 +65,7 @@ for module in pybind11_modules: )) # read the contents of introduction.rst -with open("introduction.rst", "r") as fh: +with open("@CMAKE_CURRENT_BINARY_DIR@/introduction.rst", "r") as fh: long_description = fh.read() setup( -- cgit v1.2.3 From 85c66c66e6c8dfe9ba74b3bfa0012a550e8466ec Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 3 Nov 2020 17:39:51 +0100 Subject: Fix #415 by removing all install cmake targets from examples --- src/Bitmap_cubical_complex/example/CMakeLists.txt | 2 -- src/Nerve_GIC/example/CMakeLists.txt | 3 --- src/Persistence_representations/example/CMakeLists.txt | 6 ------ src/Persistent_cohomology/example/CMakeLists.txt | 7 ------- src/Rips_complex/example/CMakeLists.txt | 5 ----- src/Skeleton_blocker/example/CMakeLists.txt | 4 ---- src/Spatial_searching/example/CMakeLists.txt | 1 - src/Subsampling/example/CMakeLists.txt | 5 ----- src/Tangential_complex/example/CMakeLists.txt | 2 -- src/Witness_complex/example/CMakeLists.txt | 7 ------- 10 files changed, 42 deletions(-) diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index dc659f2d..0ff290ef 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -6,5 +6,3 @@ if (TBB_FOUND) endif() add_test(NAME Bitmap_cubical_complex_example_random COMMAND $ "2" "100" "100") - -install(TARGETS Random_bitmap_cubical_complex DESTINATION bin) diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 1667472f..4b0f4677 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -22,7 +22,4 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") - install(TARGETS CoordGIC DESTINATION bin) - install(TARGETS FuncGIC DESTINATION bin) - endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index a7c6ef39..997f85dc 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -3,30 +3,24 @@ project(Persistence_representations_example) add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) add_test(NAME Persistence_representations_example_landscape_on_grid COMMAND $) -install(TARGETS Persistence_representations_example_landscape_on_grid DESTINATION bin) add_executable ( Persistence_representations_example_landscape persistence_landscape.cpp ) add_test(NAME Persistence_representations_example_landscape COMMAND $) -install(TARGETS Persistence_representations_example_landscape DESTINATION bin) add_executable ( Persistence_representations_example_intervals persistence_intervals.cpp ) add_test(NAME Persistence_representations_example_intervals COMMAND $ "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers") -install(TARGETS Persistence_representations_example_intervals DESTINATION bin) add_executable ( Persistence_representations_example_vectors persistence_vectors.cpp ) add_test(NAME Persistence_representations_example_vectors COMMAND $) -install(TARGETS Persistence_representations_example_vectors DESTINATION bin) add_executable ( Persistence_representations_example_heat_maps persistence_heat_maps.cpp ) add_test(NAME Persistence_representations_example_heat_maps COMMAND $) -install(TARGETS Persistence_representations_example_heat_maps DESTINATION bin) add_executable ( Sliced_Wasserstein sliced_wasserstein.cpp ) add_test(NAME Sliced_Wasserstein COMMAND $) -install(TARGETS Sliced_Wasserstein DESTINATION bin) diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index d6a92ed6..c68c6524 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -5,7 +5,6 @@ if (TBB_FOUND) target_link_libraries(plain_homology ${TBB_LIBRARIES}) endif() add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $) -install(TARGETS plain_homology DESTINATION bin) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) if (TBB_FOUND) @@ -13,7 +12,6 @@ if (TBB_FOUND) endif() add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $ "1" "0") -install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin) if(TARGET Boost::program_options) add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) @@ -23,7 +21,6 @@ if(TARGET Boost::program_options) endif() add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") - install(TARGETS rips_persistence_step_by_step DESTINATION bin) endif() if(TARGET Boost::program_options) @@ -34,7 +31,6 @@ if(TARGET Boost::program_options) endif() add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") - install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin) endif() if(TARGET Boost::program_options) @@ -47,7 +43,6 @@ if(TARGET Boost::program_options) "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0") add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $ "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") - install(TARGETS persistence_from_file DESTINATION bin) endif() if(GMP_FOUND) @@ -61,7 +56,6 @@ if(GMP_FOUND) endif(TBB_FOUND) add_test(NAME Persistent_cohomology_example_multifield_2_71 COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "2" "-q" "71") - install(TARGETS rips_multifield_persistence DESTINATION bin) endif() endif(GMPXX_FOUND) endif(GMP_FOUND) @@ -73,5 +67,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $) - install(TARGETS custom_persistence_sort DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index 244a93ec..206f4c11 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -72,8 +72,3 @@ if (DIFF_PATH) endif() -install(TARGETS Rips_complex_example_from_off DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_from_points DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_from_distance_matrix DESTINATION bin) -install(TARGETS Rips_complex_example_from_csv_distance_matrix DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_rips_from_correlation_matrix DESTINATION bin) diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt index 0e5d2f11..456612df 100644 --- a/src/Skeleton_blocker/example/CMakeLists.txt +++ b/src/Skeleton_blocker/example/CMakeLists.txt @@ -7,7 +7,3 @@ add_executable(Skeleton_blocker_example_link Skeleton_blocker_link.cpp) add_test(NAME Skeleton_blocker_example_from_simplices COMMAND $) add_test(NAME Skeleton_blocker_example_iteration COMMAND $) add_test(NAME Skeleton_blocker_example_link COMMAND $) - -install(TARGETS Skeleton_blocker_example_from_simplices DESTINATION bin) -install(TARGETS Skeleton_blocker_example_iteration DESTINATION bin) -install(TARGETS Skeleton_blocker_example_link DESTINATION bin) diff --git a/src/Spatial_searching/example/CMakeLists.txt b/src/Spatial_searching/example/CMakeLists.txt index eeb3e85f..308afa00 100644 --- a/src/Spatial_searching/example/CMakeLists.txt +++ b/src/Spatial_searching/example/CMakeLists.txt @@ -5,5 +5,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Spatial_searching_example_spatial_searching ${CGAL_LIBRARY}) add_test(NAME Spatial_searching_example_spatial_searching COMMAND $) - install(TARGETS Spatial_searching_example_spatial_searching DESTINATION bin) endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index 28aab103..dfac055c 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -14,9 +14,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Subsampling_example_sparsify_point_set COMMAND $) - install(TARGETS Subsampling_example_pick_n_random_points DESTINATION bin) - install(TARGETS Subsampling_example_choose_n_farthest_points DESTINATION bin) - install(TARGETS Subsampling_example_custom_kernel DESTINATION bin) - install(TARGETS Subsampling_example_sparsify_point_set DESTINATION bin) - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index cb1486a4..b66b5f39 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -15,6 +15,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Tangential_complex_example_with_perturb COMMAND $) - install(TARGETS Tangential_complex_example_basic DESTINATION bin) - install(TARGETS Tangential_complex_example_with_perturb DESTINATION bin) endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 2659798e..5e9736ed 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -7,8 +7,6 @@ endif() add_test(NAME Witness_complex_example_nearest_landmark_table COMMAND $) -install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) - # CGAL and Eigen3 are required for Euclidean version of Witness if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) @@ -33,10 +31,5 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Witness_complex_example_strong_off_test_torus COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") - - install(TARGETS Witness_complex_example_off DESTINATION bin) - install(TARGETS Witness_complex_example_sphere DESTINATION bin) - install(TARGETS Witness_complex_example_strong_off DESTINATION bin) - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) -- cgit v1.2.3 From ef30f636af892a2e226162af9072f0741caba886 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 3 Nov 2020 22:46:50 +0100 Subject: import matplotlib only when necessary in examples, in function of args. Tests are without matplotlib, so no need to test if present --- src/python/CMakeLists.txt | 76 ++++++++++------------ ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...arcode_persistence_from_perseus_file_example.py | 2 +- ...istence_from_correlation_matrix_file_example.py | 2 +- ...ersistence_from_distance_matrix_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...complex_plain_homology_from_off_file_example.py | 2 +- 9 files changed, 42 insertions(+), 50 deletions(-) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index c09996fe..1f101d87 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -345,29 +345,27 @@ if(PYTHONINTERP_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - # Tangential - add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" - --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + # Tangential + add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) add_gudhi_py_test(test_tangential_complex) - # Witness complex AND Subsampling - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - endif() + # Witness complex + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) # Subsampling add_gudhi_py_test(test_subsampling) @@ -422,13 +420,11 @@ if(PYTHONINTERP_FOUND) WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) - endif() add_gudhi_py_test(test_alpha_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) @@ -445,30 +441,26 @@ if(PYTHONINTERP_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - if(NUMPY_FOUND) - add_test(NAME random_cubical_complex_persistence_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" - 10 10 10) - endif() + add_test(NAME random_cubical_complex_persistence_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" + 10 10 10) add_gudhi_py_test(test_cubical_complex) # Rips - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) + add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) - endif() + add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index 727af4fa..1e0273b3 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -65,6 +64,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index e1e572df..4e97cfe3 100755 --- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -82,6 +81,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 58cb2bb5..29076c74 100755 --- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -79,6 +78,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 499171df..ee3290c6 100755 --- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import errno import os import gudhi @@ -75,6 +74,7 @@ if is_file_perseus(args.file): print("betti_numbers()=") print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_barcode(diag) plot.show() else: diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 1acb187c..ea2eb7e1 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -2,7 +2,6 @@ import sys import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -84,5 +83,6 @@ invert_diag = [ ] if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(invert_diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 79ccca96..236d085d 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -60,5 +59,6 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index 6f992508..e80233a9 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -70,6 +69,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index 85bade4a..a4b4e9f5 100755 --- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -62,6 +61,7 @@ with open(args.file, "r") as f: print(st.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: -- cgit v1.2.3 From 4d26e7220bdd9a3f95beacd8a33b0fbda461ebfa Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 3 Nov 2020 22:49:56 +0100 Subject: Revert "import matplotlib only when necessary in examples, in function of args. Tests are without matplotlib, so no need to test if present" This reverts commit ef30f636af892a2e226162af9072f0741caba886. --- src/python/CMakeLists.txt | 76 ++++++++++++---------- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...arcode_persistence_from_perseus_file_example.py | 2 +- ...istence_from_correlation_matrix_file_example.py | 2 +- ...ersistence_from_distance_matrix_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...complex_plain_homology_from_off_file_example.py | 2 +- 9 files changed, 50 insertions(+), 42 deletions(-) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 1f101d87..c09996fe 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -345,27 +345,29 @@ if(PYTHONINTERP_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - # Tangential - add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" - --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + if(MATPLOTLIB_FOUND AND NUMPY_FOUND) + # Tangential + add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) add_gudhi_py_test(test_tangential_complex) - # Witness complex - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + # Witness complex AND Subsampling + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + endif() # Subsampling add_gudhi_py_test(test_subsampling) @@ -420,11 +422,13 @@ if(PYTHONINTERP_FOUND) WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") - add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + if(MATPLOTLIB_FOUND AND NUMPY_FOUND) + add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) + endif() add_gudhi_py_test(test_alpha_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) @@ -441,26 +445,30 @@ if(PYTHONINTERP_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - add_test(NAME random_cubical_complex_persistence_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" - 10 10 10) + if(NUMPY_FOUND) + add_test(NAME random_cubical_complex_persistence_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" + 10 10 10) + endif() add_gudhi_py_test(test_cubical_complex) # Rips - add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) + if(MATPLOTLIB_FOUND AND NUMPY_FOUND) + add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) + add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) + endif() add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index 1e0273b3..727af4fa 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -3,6 +3,7 @@ import argparse import errno import os +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -64,7 +65,6 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index 4e97cfe3..e1e572df 100755 --- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,6 +3,7 @@ import argparse import errno import os +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -81,7 +82,6 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 29076c74..58cb2bb5 100755 --- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,6 +3,7 @@ import argparse import errno import os +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -78,7 +79,6 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index ee3290c6..499171df 100755 --- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import argparse +import matplotlib.pyplot as plot import errno import os import gudhi @@ -74,7 +75,6 @@ if is_file_perseus(args.file): print("betti_numbers()=") print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: - import matplotlib.pyplot as plot gudhi.plot_persistence_barcode(diag) plot.show() else: diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index ea2eb7e1..1acb187c 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -2,6 +2,7 @@ import sys import argparse +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -83,6 +84,5 @@ invert_diag = [ ] if args.no_diagram == False: - import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(invert_diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 236d085d..79ccca96 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import argparse +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -59,6 +60,5 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: - import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index e80233a9..6f992508 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -3,6 +3,7 @@ import argparse import errno import os +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -69,7 +70,6 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index a4b4e9f5..85bade4a 100755 --- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -3,6 +3,7 @@ import argparse import errno import os +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -61,7 +62,6 @@ with open(args.file, "r") as f: print(st.betti_numbers()) if args.no_diagram == False: - import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: -- cgit v1.2.3 From a539b1a800b29ee1b67eb256b8f38558a0ee6995 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Wed, 4 Nov 2020 00:27:43 +0100 Subject: Build python first This subdirectory is built sequentially and takes a very long time. Starting it first, in a parallel build, it is still the last to end, but since it started earlier it also ends earlier. Usually I build the plugin directly with python3 setup.py build_ext --inplace -j20 But I don't think there is a natural way to do that from the makefile (except for the unlimited -j), since I doubt setuptools knows how to cooperate with make, ninja, etc to share a pool of workers. --- src/CMakeLists.txt | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index cc230531..79ec42c1 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -50,6 +50,14 @@ include_directories(include) # Include module CMake subdirectories # GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake +if (WITH_GUDHI_PYTHON) + # specific for cython module + add_subdirectory(${GUDHI_PYTHON_PATH}) +else() + message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") +endif() + foreach(GUDHI_MODULE ${GUDHI_MODULES}) foreach(GUDHI_SUB_DIRECTORY ${GUDHI_SUB_DIRECTORIES}) if(EXISTS ${CMAKE_SOURCE_DIR}/${GUDHI_SUB_DIRECTORY}/${GUDHI_MODULE}/CMakeLists.txt) @@ -60,14 +68,6 @@ endforeach() add_subdirectory(GudhUI) -if (WITH_GUDHI_PYTHON) - # specific for cython module - add_subdirectory(${GUDHI_PYTHON_PATH}) -else() - message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") - set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") -endif() - message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"") -- cgit v1.2.3 From 7959734c6302e9b63e3b91780130c896127eaebe Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 4 Nov 2020 07:36:23 +0100 Subject: Revert "Fix #416 by adding full path to introduction.rst - maybe strange with conda or pip installation" This reverts commit 2d4c69d698df7e40709ec0e38463b4cf30ee388d. --- src/python/setup.py.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 1d6745fd..98d058fc 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -65,7 +65,7 @@ for module in pybind11_modules: )) # read the contents of introduction.rst -with open("@CMAKE_CURRENT_BINARY_DIR@/introduction.rst", "r") as fh: +with open("introduction.rst", "r") as fh: long_description = fh.read() setup( -- cgit v1.2.3 From 92361d9a117a33e0d922417cfbb2e1653f2537df Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 4 Nov 2020 07:58:01 +0100 Subject: import matplotlib only when necessary in examples, in function of args. Tests are without matplotlib, so no need to test if present --- src/python/CMakeLists.txt | 90 ++++++++++------------ ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...arcode_persistence_from_perseus_file_example.py | 2 +- ...istence_from_correlation_matrix_file_example.py | 2 +- ...ersistence_from_distance_matrix_file_example.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 2 +- ...complex_plain_homology_from_off_file_example.py | 2 +- 9 files changed, 49 insertions(+), 57 deletions(-) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index c09996fe..56b6876c 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -345,29 +345,27 @@ if(PYTHONINTERP_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - # Tangential - add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" - --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - - add_gudhi_py_test(test_tangential_complex) - - # Witness complex AND Subsampling - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - endif() + # Tangential + add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + + add_gudhi_py_test(test_tangential_complex) + + # Witness complex + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) # Subsampling add_gudhi_py_test(test_subsampling) @@ -422,13 +420,11 @@ if(PYTHONINTERP_FOUND) WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) - endif() + add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) add_gudhi_py_test(test_alpha_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) @@ -445,30 +441,26 @@ if(PYTHONINTERP_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - if(NUMPY_FOUND) - add_test(NAME random_cubical_complex_persistence_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" - 10 10 10) - endif() + add_test(NAME random_cubical_complex_persistence_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" + 10 10 10) add_gudhi_py_test(test_cubical_complex) # Rips - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) + add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) - endif() + add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index 727af4fa..1e0273b3 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -65,6 +64,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index e1e572df..4e97cfe3 100755 --- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -82,6 +81,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 58cb2bb5..29076c74 100755 --- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -79,6 +78,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 499171df..ee3290c6 100755 --- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import errno import os import gudhi @@ -75,6 +74,7 @@ if is_file_perseus(args.file): print("betti_numbers()=") print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_barcode(diag) plot.show() else: diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 1acb187c..ea2eb7e1 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -2,7 +2,6 @@ import sys import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -84,5 +83,6 @@ invert_diag = [ ] if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(invert_diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 79ccca96..236d085d 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -60,5 +59,6 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index 6f992508..e80233a9 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -70,6 +69,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index 85bade4a..a4b4e9f5 100755 --- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -62,6 +61,7 @@ with open(args.file, "r") as f: print(st.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: -- cgit v1.2.3 From 9ea9ae8f72c26dbe37319168cfce64afa01d0fd9 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Thu, 5 Nov 2020 01:00:56 +0100 Subject: More numpy in BettiCurve suggested by @raphaeltinarrage --- src/python/gudhi/representations/vector_methods.py | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/src/python/gudhi/representations/vector_methods.py b/src/python/gudhi/representations/vector_methods.py index 5ca127f6..6a1f61ef 100644 --- a/src/python/gudhi/representations/vector_methods.py +++ b/src/python/gudhi/representations/vector_methods.py @@ -323,22 +323,15 @@ class BettiCurve(BaseEstimator, TransformerMixin): Returns: numpy array with shape (number of diagrams) x (**resolution**): output Betti curves. """ - num_diag, Xfit = len(X), [] + Xfit = [] x_values = np.linspace(self.sample_range[0], self.sample_range[1], self.resolution) step_x = x_values[1] - x_values[0] - for i in range(num_diag): - - diagram, num_pts_in_diag = X[i], X[i].shape[0] - + for diagram in X: + diagram_int = np.clip(np.ceil((diagram[:,:2] - self.sample_range[0]) / step_x).astype(int), 0, self.resolution) bc = np.zeros(self.resolution) - for j in range(num_pts_in_diag): - [px,py] = diagram[j,:2] - min_idx = np.clip(np.ceil((px - self.sample_range[0]) / step_x).astype(int), 0, self.resolution) - max_idx = np.clip(np.ceil((py - self.sample_range[0]) / step_x).astype(int), 0, self.resolution) - for k in range(min_idx, max_idx): - bc[k] += 1 - + for interval in diagram_int: + bc[interval[0]:interval[1]] += 1 Xfit.append(np.reshape(bc,[1,-1])) Xfit = np.concatenate(Xfit, 0) -- cgit v1.2.3 From a81be6810159493933cbc0159feae191ae7d0cc3 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sat, 7 Nov 2020 11:10:09 +0100 Subject: Swap clip with int conversion This allows correct handling of infinite values. --- src/python/gudhi/representations/vector_methods.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/gudhi/representations/vector_methods.py b/src/python/gudhi/representations/vector_methods.py index 6a1f61ef..cdcb1fde 100644 --- a/src/python/gudhi/representations/vector_methods.py +++ b/src/python/gudhi/representations/vector_methods.py @@ -328,7 +328,7 @@ class BettiCurve(BaseEstimator, TransformerMixin): step_x = x_values[1] - x_values[0] for diagram in X: - diagram_int = np.clip(np.ceil((diagram[:,:2] - self.sample_range[0]) / step_x).astype(int), 0, self.resolution) + diagram_int = np.clip(np.ceil((diagram[:,:2] - self.sample_range[0]) / step_x), 0, self.resolution).astype(int) bc = np.zeros(self.resolution) for interval in diagram_int: bc[interval[0]:interval[1]] += 1 -- cgit v1.2.3 From 0022442a303f297ac773e262abd2661d2ce0a614 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sun, 8 Nov 2020 22:08:21 +0100 Subject: Test BettiCurve with infinite value + black reformatting --- src/python/test/test_representations.py | 20 +++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/src/python/test/test_representations.py b/src/python/test/test_representations.py index e5c211a0..43c914f3 100755 --- a/src/python/test/test_representations.py +++ b/src/python/test/test_representations.py @@ -39,11 +39,11 @@ def test_multiple(): d2 = BottleneckDistance(epsilon=0.00001).fit_transform(l1) d3 = pairwise_persistence_diagram_distances(l1, l1b, e=0.00001, n_jobs=4) assert d1 == pytest.approx(d2) - assert d3 == pytest.approx(d2, abs=1e-5) # Because of 0 entries (on the diagonal) + assert d3 == pytest.approx(d2, abs=1e-5) # Because of 0 entries (on the diagonal) d1 = pairwise_persistence_diagram_distances(l1, l2, metric="wasserstein", order=2, internal_p=2) d2 = WassersteinDistance(order=2, internal_p=2, n_jobs=4).fit(l2).transform(l1) print(d1.shape, d2.shape) - assert d1 == pytest.approx(d2, rel=.02) + assert d1 == pytest.approx(d2, rel=0.02) def test_dummy_atol(): @@ -53,8 +53,22 @@ def test_dummy_atol(): for weighting_method in ["cloud", "iidproba"]: for contrast in ["gaussian", "laplacian", "indicator"]: - atol_vectoriser = Atol(quantiser=KMeans(n_clusters=1, random_state=202006), weighting_method=weighting_method, contrast=contrast) + atol_vectoriser = Atol( + quantiser=KMeans(n_clusters=1, random_state=202006), + weighting_method=weighting_method, + contrast=contrast, + ) atol_vectoriser.fit([a, b, c]) atol_vectoriser(a) atol_vectoriser.transform(X=[a, b, c]) + +from gudhi.representations.vector_methods import BettiCurve + + +def test_infinity(): + a = np.array([[1.0, 8.0], [2.0, np.inf], [3.0, 4.0]]) + c = BettiCurve(20, [0.0, 10.0])(a) + assert c[1] == 0 + assert c[7] == 3 + assert c[9] == 2 -- cgit v1.2.3 From b4df19e0555c0b60c4f074ed0baf642a7d1bdc8b Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Tue, 10 Nov 2020 00:55:34 +0100 Subject: Revert change to the example It would require updating the figure. --- src/python/doc/bottleneck_distance_user.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/python/doc/bottleneck_distance_user.rst b/src/python/doc/bottleneck_distance_user.rst index 2c74c6dd..7baa76cc 100644 --- a/src/python/doc/bottleneck_distance_user.rst +++ b/src/python/doc/bottleneck_distance_user.rst @@ -35,19 +35,19 @@ The following example explains how the distance is computed: import gudhi - message = "Bottleneck distance = " + '%.1f' % gudhi.bottleneck_distance([[0., 2.]], [[1., 13.]]) + message = "Bottleneck distance = " + '%.1f' % gudhi.bottleneck_distance([[0., 0.]], [[0., 13.]]) print(message) .. testoutput:: - Bottleneck distance = 6.0 + Bottleneck distance = 6.5 .. figure:: ../../doc/Bottleneck_distance/bottleneck_distance_example.png :figclass: align-center - The point (1, 13) is at distance 6 from the diagonal and more - specifically from the point (7, 7). + The point (0, 13) is at distance 6.5 from the diagonal and more + specifically from the point (6.5, 6.5). Basic example -- cgit v1.2.3 From 53376fde3f35576af18fac33d731e8398da7522e Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Fri, 13 Nov 2020 12:39:27 +0100 Subject: Test with negative coordinates --- src/python/test/test_bottleneck_distance.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/python/test/test_bottleneck_distance.py b/src/python/test/test_bottleneck_distance.py index 6915bea8..07fcc9cc 100755 --- a/src/python/test/test_bottleneck_distance.py +++ b/src/python/test/test_bottleneck_distance.py @@ -25,3 +25,15 @@ def test_basic_bottleneck(): assert gudhi.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, abs=0.1) assert gudhi.hera.bottleneck_distance(diag1, diag2, 0) == 0.75 assert gudhi.hera.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, rel=0.1) + + import numpy as np + + # Translating both diagrams along the diagonal should not affect the distance, + # checks that negative numbers are not an issue + diag1 = np.array(diag1) - 100 + diag2 = np.array(diag2) - 100 + + assert gudhi.bottleneck_distance(diag1, diag2) == 0.75 + assert gudhi.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, abs=0.1) + assert gudhi.hera.bottleneck_distance(diag1, diag2, 0) == 0.75 + assert gudhi.hera.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, rel=0.1) -- cgit v1.2.3 From 3df4648996a4c30f4587115c57aee13ba3c96da7 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Fri, 13 Nov 2020 14:40:01 +0100 Subject: Add tensorflow-addons as test requirement --- .github/test-requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/test-requirements.txt b/.github/test-requirements.txt index 7d69c0b9..688a2a11 100644 --- a/.github/test-requirements.txt +++ b/.github/test-requirements.txt @@ -8,6 +8,7 @@ scipy scikit-learn POT tensorflow +tensorflow-addons torch<1.5 pykeops hnswlib -- cgit v1.2.3