diff options
Diffstat (limited to 'src/python')
| -rw-r--r-- | src/python/CMakeLists.txt | 6 | ||||
| -rwxr-xr-x | src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py | 2 | ||||
| -rw-r--r-- | src/python/gudhi/hera/wasserstein.cc | 2 | ||||
| -rw-r--r-- | src/python/gudhi/persistence_graphical_tools.py | 2 | ||||
| -rw-r--r-- | src/python/gudhi/simplex_tree.pxd | 4 | ||||
| -rw-r--r-- | src/python/gudhi/simplex_tree.pyx | 3 | ||||
| -rw-r--r-- | src/python/gudhi/wasserstein/barycenter.py | 6 | ||||
| -rw-r--r-- | src/python/include/Persistent_cohomology_interface.h | 40 | ||||
| -rw-r--r-- | src/python/include/Simplex_tree_interface.h | 30 | ||||
| -rwxr-xr-x | src/python/test/test_simplex_tree.py | 6 | ||||
| -rwxr-xr-x | src/python/test/test_subsampling.py | 4 |
11 files changed, 59 insertions, 46 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 54221151..af0b6115 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -329,9 +329,9 @@ if(PYTHONINTERP_FOUND) if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") # User warning - Sphinx is a static pages generator, and configured to work fine with user_version - # Images and biblio warnings because not found on developper version + # Images and biblio warnings because not found on developer version if (GUDHI_PYTHON_PATH STREQUAL "src/python") - set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss") + set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developer version. Images and biblio will miss") endif() # sphinx target requires gudhi.so, because conf.py reads gudhi version from it add_custom_target(sphinx @@ -484,7 +484,7 @@ if(PYTHONINTERP_FOUND) add_gudhi_py_test(test_euclidean_witness_complex) # Datasets generators - add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independant from CGAL ? + add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independent from CGAL ? endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) 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..0b35dbc5 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 @@ -40,7 +40,7 @@ parser.add_argument( args = parser.parse_args() if not (-1.0 < args.min_edge_correlation < 1.0): - print("Wrong value of the treshold corelation (should be between -1 and 1).") + print("Wrong value of the threshold corelation (should be between -1 and 1).") sys.exit(1) print("#####################################################################") diff --git a/src/python/gudhi/hera/wasserstein.cc b/src/python/gudhi/hera/wasserstein.cc index 1a21f02f..fa0cf8aa 100644 --- a/src/python/gudhi/hera/wasserstein.cc +++ b/src/python/gudhi/hera/wasserstein.cc @@ -29,7 +29,7 @@ double wasserstein_distance( if(std::isinf(internal_p)) internal_p = hera::get_infinity<double>(); params.internal_p = internal_p; params.delta = delta; - // The extra parameters are purposedly not exposed for now. + // The extra parameters are purposely not exposed for now. return hera::wasserstein_dist(diag1, diag2, params); } diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py index 7ed11360..21275cdd 100644 --- a/src/python/gudhi/persistence_graphical_tools.py +++ b/src/python/gudhi/persistence_graphical_tools.py @@ -332,7 +332,7 @@ def plot_persistence_diagram( axes.plot([axis_start, axis_end], [infinity, infinity], linewidth=1.0, color="k", alpha=alpha) # Infinity label yt = axes.get_yticks() - yt = yt[np.where(yt < axis_end)] # to avoid ploting ticklabel higher than infinity + yt = yt[np.where(yt < axis_end)] # to avoid plotting ticklabel higher than infinity yt = np.append(yt, infinity) ytl = ["%.3f" % e for e in yt] # to avoid float precision error ytl[-1] = r"$+\infty$" diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 4f229663..5642f82d 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -63,7 +63,6 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": bool prune_above_filtration(double filtration) nogil 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 Simplex_tree_interface_full_featured* collapse_edges(int nb_collapse_iteration) nogil except + void reset_filtration(double filtration, int dimension) nogil bint operator==(Simplex_tree_interface_full_featured) nogil @@ -81,7 +80,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data) cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": - cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>": + cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>>": Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max) nogil void compute_persistence(int homology_coeff_field, double min_persistence) nogil except + vector[pair[int, pair[double, double]]] get_persistence() nogil @@ -92,3 +91,4 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": vector[pair[vector[int], vector[int]]] persistence_pairs() nogil pair[vector[vector[int]], vector[vector[int]]] lower_star_generators() nogil pair[vector[vector[int]], vector[vector[int]]] flag_generators() nogil + vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(double min_persistence) nogil diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 2c53a872..521a7763 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -474,8 +474,7 @@ cdef class SimplexTree: del self.pcohptr self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), False) self.pcohptr.compute_persistence(homology_coeff_field, -1.) - persistence_result = self.pcohptr.get_persistence() - return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result, min_persistence) + return self.pcohptr.compute_extended_persistence_subdiagrams(min_persistence) def expansion_with_blocker(self, max_dim, blocker_func): """Expands the Simplex_tree containing only a graph. Simplices corresponding to cliques in the graph are added diff --git a/src/python/gudhi/wasserstein/barycenter.py b/src/python/gudhi/wasserstein/barycenter.py index d67bcde7..bb6e641e 100644 --- a/src/python/gudhi/wasserstein/barycenter.py +++ b/src/python/gudhi/wasserstein/barycenter.py @@ -37,7 +37,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False): :param init: The initial value for barycenter estimate. If ``None``, init is made on a random diagram from the dataset. Otherwise, it can be an ``int`` (then initialization is made on ``pdiagset[init]``) - or a `(n x 2)` ``numpy.array`` enconding a persistence diagram with `n` points. + or a `(n x 2)` ``numpy.array`` encoding a persistence diagram with `n` points. :type init: ``int``, or (n x 2) ``np.array`` :param verbose: if ``True``, returns additional information about the barycenter. :type verbose: boolean @@ -45,7 +45,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False): (local minimum of the energy function). If ``pdiagset`` is empty, returns ``None``. If verbose, returns a couple ``(Y, log)`` where ``Y`` is the barycenter estimate, - and ``log`` is a ``dict`` that contains additional informations: + and ``log`` is a ``dict`` that contains additional information: - `"groupings"`, a list of list of pairs ``(i,j)``. Namely, ``G[k] = [...(i, j)...]``, where ``(i,j)`` indicates that `pdiagset[k][i]`` is matched to ``Y[j]`` if ``i = -1`` or ``j = -1``, it means they represent the diagonal. @@ -73,7 +73,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False): nb_iter = 0 - converged = False # stoping criterion + converged = False # stopping criterion while not converged: nb_iter += 1 K = len(Y) # current nb of points in Y (some might be on diagonal) diff --git a/src/python/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h index e5a3dfba..945378a0 100644 --- a/src/python/include/Persistent_cohomology_interface.h +++ b/src/python/include/Persistent_cohomology_interface.h @@ -12,6 +12,8 @@ #define INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_ #include <gudhi/Persistent_cohomology.h> +#include <gudhi/Simplex_tree.h> // for Extended_simplex_type + #include <cstdlib> #include <vector> @@ -223,6 +225,44 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol return out; } + using Filtration_value = typename FilteredComplex::Filtration_value; + using Birth_death = std::pair<Filtration_value, Filtration_value>; + using Persistence_subdiagrams = std::vector<std::vector<std::pair<int, Birth_death>>>; + + Persistence_subdiagrams compute_extended_persistence_subdiagrams(Filtration_value min_persistence){ + Persistence_subdiagrams pers_subs(4); + auto const& persistent_pairs = Base::get_persistent_pairs(); + for (auto pair : persistent_pairs) { + std::pair<Filtration_value, Extended_simplex_type> px = stptr_->decode_extended_filtration(stptr_->filtration(get<0>(pair)), + stptr_->efd); + std::pair<Filtration_value, Extended_simplex_type> py = stptr_->decode_extended_filtration(stptr_->filtration(get<1>(pair)), + stptr_->efd); + std::pair<int, Birth_death> pd_point = std::make_pair(stptr_->dimension(get<0>(pair)), + std::make_pair(px.first, py.first)); + if(std::abs(px.first - py.first) > min_persistence){ + //Ordinary + if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){ + pers_subs[0].push_back(pd_point); + } + // Relative + else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){ + pers_subs[1].push_back(pd_point); + } + else{ + // Extended+ + if (px.first < py.first){ + pers_subs[2].push_back(pd_point); + } + //Extended- + else{ + pers_subs[3].push_back(pd_point); + } + } + } + } + return pers_subs; + } + private: // A copy FilteredComplex* stptr_; diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index 7f9b0067..3848c5ad 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -132,36 +132,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { return; } - std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> compute_extended_persistence_subdiagrams(const std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>& dgm, Filtration_value min_persistence){ - std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> new_dgm(4); - for (unsigned int i = 0; i < dgm.size(); i++){ - std::pair<Filtration_value, Extended_simplex_type> px = this->decode_extended_filtration(dgm[i].second.first, this->efd); - std::pair<Filtration_value, Extended_simplex_type> py = this->decode_extended_filtration(dgm[i].second.second, this->efd); - std::pair<int, std::pair<Filtration_value, Filtration_value>> pd_point = std::make_pair(dgm[i].first, std::make_pair(px.first, py.first)); - if(std::abs(px.first - py.first) > min_persistence){ - //Ordinary - if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){ - new_dgm[0].push_back(pd_point); - } - // Relative - else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){ - new_dgm[1].push_back(pd_point); - } - else{ - // Extended+ - if (px.first < py.first){ - new_dgm[2].push_back(pd_point); - } - //Extended- - else{ - new_dgm[3].push_back(pd_point); - } - } - } - } - return new_dgm; - } - Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) { using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>; std::vector<Filtered_edge> edges; diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 688f4fd6..54bafed5 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -320,6 +320,10 @@ def test_extend_filtration(): ] dgms = st.extended_persistence(min_persistence=-1.) + assert len(dgms) == 4 + # Sort by (death-birth) descending - we are only interested in those with the longest life span + for idx in range(4): + dgms[idx] = sorted(dgms[idx], key=lambda x:(-abs(x[1][0]-x[1][1]))) assert dgms[0][0][1][0] == pytest.approx(2.) assert dgms[0][0][1][1] == pytest.approx(3.) @@ -528,7 +532,7 @@ def test_expansion_with_blocker(): def blocker(simplex): try: - # Block all simplices that countains vertex 6 + # Block all simplices that contain vertex 6 simplex.index(6) print(simplex, ' is blocked') return True diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py index 4019852e..3431f372 100755 --- a/src/python/test/test_subsampling.py +++ b/src/python/test/test_subsampling.py @@ -91,7 +91,7 @@ def test_simple_choose_n_farthest_points_randomed(): assert gudhi.choose_n_farthest_points(points=[], nb_points=1) == [] assert gudhi.choose_n_farthest_points(points=point_set, nb_points=0) == [] - # Go furter than point set on purpose + # Go further than point set on purpose for iter in range(1, 10): sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=iter) for sub in sub_set: @@ -117,7 +117,7 @@ def test_simple_pick_n_random_points(): assert gudhi.pick_n_random_points(points=[], nb_points=1) == [] assert gudhi.pick_n_random_points(points=point_set, nb_points=0) == [] - # Go furter than point set on purpose + # Go further than point set on purpose for iter in range(1, 10): sub_set = gudhi.pick_n_random_points(points=point_set, nb_points=iter) for sub in sub_set: |