Index Symbols | _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y Symbols **kwargs (gudhi.representations.kernel_methods.pairwise_persistence_diagram_kernels parameter) (gudhi.representations.metrics.pairwise_persistence_diagram_distances parameter) **params (gudhi.cover_complex.GraphInducedComplex.set_params parameter) (gudhi.cover_complex.MapperComplex.set_params parameter) (gudhi.cover_complex.NerveComplex.set_params parameter) _ __call__() (gudhi.point_cloud.timedelay.TimeDelayEmbedding method) (gudhi.representations.kernel_methods.PersistenceFisherKernel method) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel method) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel method) (gudhi.representations.kernel_methods.SlicedWassersteinKernel method) (gudhi.representations.metrics.BottleneckDistance method) (gudhi.representations.metrics.PersistenceFisherDistance method) (gudhi.representations.metrics.SlicedWassersteinDistance method) (gudhi.representations.metrics.WassersteinDistance method) (gudhi.representations.preprocessing.BirthPersistenceTransform method) (gudhi.representations.preprocessing.DiagramScaler method) (gudhi.representations.preprocessing.DiagramSelector method) (gudhi.representations.preprocessing.Padding method) (gudhi.representations.preprocessing.ProminentPoints method) (gudhi.representations.vector_methods.Atol method) (gudhi.representations.vector_methods.BettiCurve method) (gudhi.representations.vector_methods.ComplexPolynomial method) (gudhi.representations.vector_methods.Entropy method) (gudhi.representations.vector_methods.Landscape method) (gudhi.representations.vector_methods.PersistenceImage method) (gudhi.representations.vector_methods.Silhouette method) (gudhi.representations.vector_methods.TopologicalVector method) __eq__() (gudhi.SimplexTree method) __getstate__() (gudhi.SimplexTree method) __init__() (gudhi.AlphaComplex method) (gudhi.clustering.tomato.Tomato method) (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) (gudhi.CoverComplex method) (gudhi.CubicalComplex method) (gudhi.dtm_rips_complex.DTMRipsComplex method) (gudhi.EuclideanStrongWitnessComplex method) (gudhi.EuclideanWitnessComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.point_cloud.dtm.DistanceToMeasure method) (gudhi.point_cloud.dtm.DTMDensity method) (gudhi.point_cloud.knn.KNearestNeighbors method) (gudhi.point_cloud.timedelay.TimeDelayEmbedding method) (gudhi.representations.kernel_methods.PersistenceFisherKernel method) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel method) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel method) (gudhi.representations.kernel_methods.SlicedWassersteinKernel method) (gudhi.representations.metrics.BottleneckDistance method) (gudhi.representations.metrics.PersistenceFisherDistance method) (gudhi.representations.metrics.SlicedWassersteinDistance method) (gudhi.representations.metrics.WassersteinDistance method) (gudhi.representations.preprocessing.BirthPersistenceTransform method) (gudhi.representations.preprocessing.Clamping method) (gudhi.representations.preprocessing.DiagramScaler method) (gudhi.representations.preprocessing.DiagramSelector method) (gudhi.representations.preprocessing.DimensionSelector method) (gudhi.representations.preprocessing.Padding method) (gudhi.representations.preprocessing.ProminentPoints method) (gudhi.representations.vector_methods.Atol method) (gudhi.representations.vector_methods.BettiCurve method) (gudhi.representations.vector_methods.ComplexPolynomial method) (gudhi.representations.vector_methods.Entropy method) (gudhi.representations.vector_methods.Landscape method) (gudhi.representations.vector_methods.PersistenceImage method) (gudhi.representations.vector_methods.Silhouette method) (gudhi.representations.vector_methods.TopologicalVector method) (gudhi.RipsComplex method) (gudhi.SimplexTree method) (gudhi.sklearn.cubical_persistence.CubicalPersistence method) (gudhi.sklearn.rips_persistence.RipsPersistence method) (gudhi.StrongWitnessComplex method) (gudhi.TangentialComplex method) (gudhi.tensorflow.CubicalLayer method) (gudhi.tensorflow.LowerStarSimplexTreeLayer method) (gudhi.tensorflow.perslay.FlatPerslayPhi method) (gudhi.tensorflow.perslay.GaussianMixturePerslayWeight method) (gudhi.tensorflow.perslay.GaussianPerslayPhi method) (gudhi.tensorflow.perslay.GridPerslayWeight method) (gudhi.tensorflow.perslay.Perslay method) (gudhi.tensorflow.perslay.PowerPerslayWeight method) (gudhi.tensorflow.perslay.TentPerslayPhi method) (gudhi.tensorflow.RipsLayer method) (gudhi.weighted_rips_complex.WeightedRipsComplex method) (gudhi.WitnessComplex method) __new__() (gudhi.AlphaComplex method) (gudhi.CoverComplex method) (gudhi.CubicalComplex method) (gudhi.EuclideanStrongWitnessComplex method) (gudhi.EuclideanWitnessComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.RipsComplex method) (gudhi.SimplexTree method) (gudhi.StrongWitnessComplex method) (gudhi.TangentialComplex method) (gudhi.WitnessComplex method) __setstate__() (gudhi.SimplexTree method) A accept_license (gudhi.datasets.remote.fetch_bunny parameter) (gudhi.datasets.remote.fetch_daily_activities parameter) all_cells() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) alpha (gudhi.CoverComplex.compute_distance_from_confidence_level parameter) (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_diagram parameter) AlphaComplex (class in gudhi) ambient_dim (gudhi.datasets.generators.points.sphere parameter) assign_filtration() (gudhi.SimplexTree method) assignments (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.cover_complex.NerveComplex.fit parameter) (gudhi.cover_complex.NerveComplex.set_fit_request parameter) (gudhi.CoverComplex.set_cover_from_range parameter) Atol (class in gudhi.representations.vector_methods) axes (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_density parameter) (gudhi.plot_persistence_diagram parameter) B band (gudhi.plot_persistence_diagram parameter) bandwidth (gudhi.representations.kernel_methods.PersistenceFisherKernel parameter) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel parameter) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel parameter) (gudhi.representations.kernel_methods.SlicedWassersteinKernel parameter) (gudhi.representations.metrics.PersistenceFisherDistance parameter) (gudhi.representations.vector_methods.PersistenceImage parameter) bandwidth_fisher (gudhi.representations.kernel_methods.PersistenceFisherKernel parameter) beta (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.cover_complex.MapperComplex parameter) (gudhi.cover_complex.MapperComplex.estimate_scale parameter) (gudhi.cover_complex.MapperComplex.get_optimal_parameters_for_agglomerative_clustering parameter) betti_numbers() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) BettiCurve (class in gudhi.representations.vector_methods) BirthPersistenceTransform (class in gudhi.representations.preprocessing) blocker_func (gudhi.SimplexTree.expansion_with_blocker parameter) bottleneck_distance() (in module gudhi) (in module gudhi.hera) BottleneckDistance (class in gudhi.representations.metrics) build() (gudhi.tensorflow.perslay.FlatPerslayPhi method) (gudhi.tensorflow.perslay.GaussianMixturePerslayWeight method) (gudhi.tensorflow.perslay.GaussianPerslayPhi method) (gudhi.tensorflow.perslay.GridPerslayWeight method) (gudhi.tensorflow.perslay.Perslay method) (gudhi.tensorflow.perslay.PowerPerslayWeight method) (gudhi.tensorflow.perslay.TentPerslayPhi method) bw_method (gudhi.plot_persistence_density parameter) C C (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.cover_complex.MapperComplex parameter) (gudhi.cover_complex.MapperComplex.estimate_scale parameter) (gudhi.cover_complex.MapperComplex.get_optimal_parameters_for_agglomerative_clustering parameter) c (gudhi.CoverComplex.subcolor parameter) (gudhi.CoverComplex.subpopulation parameter) call() (gudhi.tensorflow.CubicalLayer method) (gudhi.tensorflow.LowerStarSimplexTreeLayer method) (gudhi.tensorflow.perslay.FlatPerslayPhi method) (gudhi.tensorflow.perslay.GaussianMixturePerslayWeight method) (gudhi.tensorflow.perslay.GaussianPerslayPhi method) (gudhi.tensorflow.perslay.GridPerslayWeight method) (gudhi.tensorflow.perslay.Perslay method) (gudhi.tensorflow.perslay.PowerPerslayWeight method) (gudhi.tensorflow.perslay.TentPerslayPhi method) (gudhi.tensorflow.RipsLayer method) children_ (gudhi.clustering.tomato.Tomato attribute) choose_n_farthest_points() (in module gudhi.subsampling) Clamping (class in gudhi.representations.preprocessing) clear_data_home() (in module gudhi.datasets.remote) cloud (gudhi.CoverComplex.set_point_cloud_from_range parameter) clustering (gudhi.cover_complex.MapperComplex parameter) cmap (gudhi.plot_persistence_density parameter) codimension (gudhi.SimplexTree.get_cofaces parameter) cofaces_of_persistence_pairs() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) collapse_edges() (gudhi.SimplexTree method) color (gudhi.cover_complex.GraphInducedComplex.fit parameter) (gudhi.cover_complex.GraphInducedComplex.set_fit_request parameter) (gudhi.cover_complex.NerveComplex.fit parameter) (gudhi.cover_complex.NerveComplex.set_fit_request parameter) (gudhi.CoverComplex.set_color_from_range parameter) color_file_name (gudhi.CoverComplex.set_color_from_file parameter) color_name (gudhi.cover_complex.GraphInducedComplex.save_to_dot parameter) (gudhi.cover_complex.GraphInducedComplex.save_to_html parameter) (gudhi.cover_complex.GraphInducedComplex.save_to_txt parameter) (gudhi.cover_complex.MapperComplex.save_to_dot parameter) (gudhi.cover_complex.MapperComplex.save_to_html parameter) (gudhi.cover_complex.MapperComplex.save_to_txt parameter) (gudhi.cover_complex.NerveComplex.save_to_dot parameter) (gudhi.cover_complex.NerveComplex.save_to_html parameter) (gudhi.cover_complex.NerveComplex.save_to_txt parameter) colormap (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_diagram parameter) colors (gudhi.cover_complex.MapperComplex.fit parameter) (gudhi.cover_complex.MapperComplex.set_fit_request parameter) ComplexPolynomial (class in gudhi.representations.vector_methods) compute_confidence_level_from_distance() (gudhi.CoverComplex method) compute_distance_from_confidence_level() (gudhi.CoverComplex method) compute_distribution() (gudhi.CoverComplex method) compute_p_value() (gudhi.CoverComplex method) compute_PD() (gudhi.CoverComplex method) compute_persistence() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) compute_tangential_complex() (gudhi.TangentialComplex method) constant (gudhi.CoverComplex.set_subsampling parameter) (gudhi.tensorflow.perslay.PowerPerslayWeight parameter) contrast (gudhi.representations.vector_methods.Atol parameter) copy() (gudhi.SimplexTree method) cover (gudhi.cover_complex.GraphInducedComplex parameter) cover_file_name (gudhi.CoverComplex.set_cover_from_file parameter) cover_name (gudhi.cover_complex.GraphInducedComplex.save_to_html parameter) (gudhi.cover_complex.GraphInducedComplex.save_to_txt parameter) (gudhi.cover_complex.MapperComplex.save_to_html parameter) (gudhi.cover_complex.MapperComplex.save_to_txt parameter) (gudhi.cover_complex.NerveComplex.save_to_html parameter) (gudhi.cover_complex.NerveComplex.save_to_txt parameter) CoverComplex (class in gudhi) create_from_array() (gudhi.SimplexTree static method) create_simplex_tree() (gudhi.AlphaComplex method) (gudhi.CoverComplex method) (gudhi.EuclideanStrongWitnessComplex method) (gudhi.EuclideanWitnessComplex method) (gudhi.RipsComplex method) (gudhi.StrongWitnessComplex method) (gudhi.TangentialComplex method) (gudhi.weighted_rips_complex.WeightedRipsComplex method) (gudhi.WitnessComplex method) csv_file (gudhi.read_lower_triangular_matrix_from_csv_file parameter) ctorus() (in module gudhi.datasets.generators.points) CubicalComplex (class in gudhi) CubicalLayer (class in gudhi.tensorflow) CubicalPersistence (class in gudhi.sklearn.cubical_persistence) D data_home (gudhi.datasets.remote.clear_data_home parameter) data_name (gudhi.cover_complex.GraphInducedComplex.save_to_html parameter) (gudhi.cover_complex.GraphInducedComplex.save_to_txt parameter) (gudhi.cover_complex.MapperComplex.save_to_html parameter) (gudhi.cover_complex.MapperComplex.save_to_txt parameter) (gudhi.cover_complex.NerveComplex.save_to_html parameter) (gudhi.cover_complex.NerveComplex.save_to_txt parameter) deep (gudhi.cover_complex.GraphInducedComplex.get_params parameter) (gudhi.cover_complex.MapperComplex.get_params parameter) (gudhi.cover_complex.NerveComplex.get_params parameter) default_filtration_value (gudhi.AlphaComplex.create_simplex_tree parameter) delay (gudhi.point_cloud.timedelay.TimeDelayEmbedding parameter) delta (gudhi.hera.bottleneck_distance parameter) (gudhi.hera.wasserstein_distance parameter) (gudhi.representations.metrics.WassersteinDistance parameter) density_type (gudhi.clustering.tomato.Tomato parameter) diag (gudhi.representations.preprocessing.BirthPersistenceTransform.__call__ parameter) (gudhi.representations.preprocessing.DiagramScaler.__call__ parameter) (gudhi.representations.preprocessing.DiagramSelector.__call__ parameter) (gudhi.representations.preprocessing.Padding.__call__ parameter) (gudhi.representations.preprocessing.ProminentPoints.__call__ parameter) (gudhi.representations.vector_methods.ComplexPolynomial.__call__ parameter) (gudhi.representations.vector_methods.Entropy.__call__ parameter) (gudhi.representations.vector_methods.Landscape.__call__ parameter) (gudhi.representations.vector_methods.PersistenceImage.__call__ parameter) (gudhi.representations.vector_methods.Silhouette.__call__ parameter) (gudhi.representations.vector_methods.TopologicalVector.__call__ parameter) diag1 (gudhi.representations.kernel_methods.PersistenceFisherKernel.__call__ parameter) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel.__call__ parameter) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel.__call__ parameter) (gudhi.representations.kernel_methods.SlicedWassersteinKernel.__call__ parameter) (gudhi.representations.metrics.BottleneckDistance.__call__ parameter) (gudhi.representations.metrics.PersistenceFisherDistance.__call__ parameter) (gudhi.representations.metrics.SlicedWassersteinDistance.__call__ parameter) (gudhi.representations.metrics.WassersteinDistance.__call__ parameter) diag2 (gudhi.representations.kernel_methods.PersistenceFisherKernel.__call__ parameter) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel.__call__ parameter) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel.__call__ parameter) (gudhi.representations.kernel_methods.SlicedWassersteinKernel.__call__ parameter) (gudhi.representations.metrics.BottleneckDistance.__call__ parameter) (gudhi.representations.metrics.PersistenceFisherDistance.__call__ parameter) (gudhi.representations.metrics.SlicedWassersteinDistance.__call__ parameter) (gudhi.representations.metrics.WassersteinDistance.__call__ parameter) diagram_ (gudhi.clustering.tomato.Tomato attribute) diagram_1 (gudhi.bottleneck_distance parameter) diagram_2 (gudhi.bottleneck_distance parameter) diagrams (gudhi.tensorflow.perslay.FlatPerslayPhi.call parameter) (gudhi.tensorflow.perslay.GaussianMixturePerslayWeight.call parameter) (gudhi.tensorflow.perslay.GaussianPerslayPhi.call parameter) (gudhi.tensorflow.perslay.GridPerslayWeight.call parameter) (gudhi.tensorflow.perslay.Perslay.call parameter) (gudhi.tensorflow.perslay.PowerPerslayWeight.call parameter) (gudhi.tensorflow.perslay.TentPerslayPhi.call parameter) DiagramScaler (class in gudhi.representations.preprocessing) DiagramSelector (class in gudhi.representations.preprocessing) dim (gudhi.clustering.tomato.Tomato parameter) (gudhi.datasets.generators.points.ctorus parameter) (gudhi.datasets.generators.points.torus parameter) (gudhi.point_cloud.dtm.DTMDensity parameter) (gudhi.point_cloud.timedelay.TimeDelayEmbedding parameter) dimension (gudhi.CubicalComplex.persistence_intervals_in_dimension parameter) (gudhi.PeriodicCubicalComplex.persistence_intervals_in_dimension parameter) (gudhi.plot_persistence_density parameter) (gudhi.SimplexTree.get_skeleton parameter) (gudhi.SimplexTree.persistence_intervals_in_dimension parameter) (gudhi.SimplexTree.prune_above_dimension parameter) (gudhi.SimplexTree.set_dimension parameter) dimension() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) dimensions (gudhi.CubicalComplex parameter), [1] (gudhi.PeriodicCubicalComplex parameter), [1] DimensionSelector (class in gudhi.representations.preprocessing) distance (gudhi.CoverComplex.compute_confidence_level_from_distance parameter) distance_matrix (gudhi.CoverComplex.set_distances_from_range parameter) (gudhi.dtm_rips_complex.DTMRipsComplex parameter) (gudhi.RipsComplex parameter) (gudhi.weighted_rips_complex.WeightedRipsComplex parameter) DistanceToMeasure (class in gudhi.point_cloud.dtm) DTMDensity (class in gudhi.point_cloud.dtm) DTMRipsComplex (class in gudhi.dtm_rips_complex) E e (gudhi.bottleneck_distance parameter) edges (gudhi.SimplexTree.insert_edges_from_coo_matrix parameter) enable_autodiff (gudhi.point_cloud.knn.KNearestNeighbors parameter) (gudhi.wasserstein.wasserstein_distance parameter) Entropy (class in gudhi.representations.vector_methods) eps (gudhi.clustering.tomato.Tomato parameter) (gudhi.point_cloud.knn.KNearestNeighbors parameter) eps_color (gudhi.cover_complex.GraphInducedComplex.save_to_dot parameter) (gudhi.cover_complex.MapperComplex.save_to_dot parameter) (gudhi.cover_complex.NerveComplex.save_to_dot parameter) eps_size (gudhi.cover_complex.GraphInducedComplex.save_to_dot parameter) (gudhi.cover_complex.MapperComplex.save_to_dot parameter) (gudhi.cover_complex.NerveComplex.save_to_dot parameter) epsilon (gudhi.representations.metrics.BottleneckDistance parameter) estimate_scale() (gudhi.cover_complex.MapperComplex method) EuclideanStrongWitnessComplex (class in gudhi) EuclideanWitnessComplex (class in gudhi) expansion() (gudhi.SimplexTree method) expansion_with_blocker() (gudhi.SimplexTree method) extend_filtration() (gudhi.SimplexTree method) extended_persistence() (gudhi.SimplexTree method) F F (gudhi.tensorflow.LowerStarSimplexTreeLayer.call parameter) fast (gudhi.subsampling.choose_n_farthest_points parameter) fetch_bunny() (in module gudhi.datasets.remote) fetch_daily_activities() (in module gudhi.datasets.remote) fetch_spiral_2d() (in module gudhi.datasets.remote) file_name (gudhi.cover_complex.GraphInducedComplex.save_to_dot parameter) (gudhi.cover_complex.GraphInducedComplex.save_to_html parameter) (gudhi.cover_complex.GraphInducedComplex.save_to_txt parameter) (gudhi.cover_complex.MapperComplex.save_to_dot parameter) (gudhi.cover_complex.MapperComplex.save_to_html parameter) (gudhi.cover_complex.MapperComplex.save_to_txt parameter) (gudhi.cover_complex.NerveComplex.save_to_dot parameter) (gudhi.cover_complex.NerveComplex.save_to_html parameter) (gudhi.cover_complex.NerveComplex.save_to_txt parameter) file_path (gudhi.datasets.remote.fetch_bunny parameter) (gudhi.datasets.remote.fetch_daily_activities parameter) (gudhi.datasets.remote.fetch_spiral_2d parameter) filter (gudhi.cover_complex.GraphInducedComplex.fit parameter) (gudhi.cover_complex.GraphInducedComplex.set_fit_request parameter) filter_bnds (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.cover_complex.MapperComplex parameter) filters (gudhi.cover_complex.MapperComplex.fit parameter) (gudhi.cover_complex.MapperComplex.set_fit_request parameter) filtration (gudhi.SimplexTree.assign_filtration parameter) (gudhi.SimplexTree.insert parameter) (gudhi.SimplexTree.prune_above_filtration parameter) (gudhi.SimplexTree.reset_filtration parameter) filtration() (gudhi.SimplexTree method) filtrations (gudhi.SimplexTree.create_from_array parameter) find() (gudhi.SimplexTree method) find_simplices() (gudhi.CoverComplex method) fit() (gudhi.clustering.tomato.Tomato method) (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) (gudhi.point_cloud.dtm.DistanceToMeasure method) (gudhi.point_cloud.dtm.DTMDensity method) (gudhi.point_cloud.knn.KNearestNeighbors method) (gudhi.representations.kernel_methods.PersistenceFisherKernel method) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel method) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel method) (gudhi.representations.kernel_methods.SlicedWassersteinKernel method) (gudhi.representations.metrics.BottleneckDistance method) (gudhi.representations.metrics.PersistenceFisherDistance method) (gudhi.representations.metrics.SlicedWassersteinDistance method) (gudhi.representations.metrics.WassersteinDistance method) (gudhi.representations.preprocessing.BirthPersistenceTransform method) (gudhi.representations.preprocessing.Clamping method) (gudhi.representations.preprocessing.DiagramScaler method) (gudhi.representations.preprocessing.DiagramSelector method) (gudhi.representations.preprocessing.DimensionSelector method) (gudhi.representations.preprocessing.Padding method) (gudhi.representations.preprocessing.ProminentPoints method) (gudhi.representations.vector_methods.Atol method) (gudhi.representations.vector_methods.BettiCurve method) (gudhi.representations.vector_methods.ComplexPolynomial method) (gudhi.representations.vector_methods.Entropy method) (gudhi.representations.vector_methods.Landscape method) (gudhi.representations.vector_methods.PersistenceImage method) (gudhi.representations.vector_methods.Silhouette method) (gudhi.representations.vector_methods.TopologicalVector method) (gudhi.sklearn.cubical_persistence.CubicalPersistence method) (gudhi.sklearn.rips_persistence.RipsPersistence method) fit_predict() (gudhi.clustering.tomato.Tomato method) fit_transform() (gudhi.point_cloud.dtm.DistanceToMeasure method) (gudhi.point_cloud.dtm.DTMDensity method) (gudhi.point_cloud.knn.KNearestNeighbors method) (gudhi.representations.vector_methods.BettiCurve method) fix_inconsistencies_using_perturbation() (gudhi.TangentialComplex method) flag_persistence_generators() (gudhi.SimplexTree method) FlatPerslayPhi (class in gudhi.tensorflow.perslay) fname (gudhi.write_points_to_off_file parameter) fontsize (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_density parameter) (gudhi.plot_persistence_diagram parameter) from_value (gudhi.CubicalComplex.persistent_betti_numbers parameter) (gudhi.PeriodicCubicalComplex.persistent_betti_numbers parameter) (gudhi.SimplexTree.persistent_betti_numbers parameter) func_file_name (gudhi.CoverComplex.set_function_from_file parameter) function (gudhi.CoverComplex.set_function_from_range parameter) G g (gudhi.CoverComplex.set_gain parameter) gain (gudhi.cover_complex.GraphInducedComplex parameter) gains (gudhi.cover_complex.MapperComplex parameter) GaussianMixturePerslayWeight (class in gudhi.tensorflow.perslay) GaussianPerslayPhi (class in gudhi.tensorflow.perslay) gaussians (gudhi.tensorflow.perslay.GaussianMixturePerslayWeight parameter) get_boundaries() (gudhi.SimplexTree method) get_cofaces() (gudhi.SimplexTree method) get_filtration() (gudhi.SimplexTree method) get_float_relative_precision() (gudhi.AlphaComplex static method) get_metadata_routing() (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) get_networkx() (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) get_optimal_parameters_for_agglomerative_clustering() (gudhi.cover_complex.MapperComplex method) get_params() (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) get_point() (gudhi.AlphaComplex method) (gudhi.EuclideanStrongWitnessComplex method) (gudhi.EuclideanWitnessComplex method) (gudhi.TangentialComplex method) get_simplices() (gudhi.SimplexTree method) get_skeleton() (gudhi.SimplexTree method) get_star() (gudhi.SimplexTree method) graph (gudhi.cover_complex.GraphInducedComplex parameter) graph_file_name (gudhi.CoverComplex.set_graph_from_file parameter) graph_type (gudhi.clustering.tomato.Tomato parameter) GraphInducedComplex (class in gudhi.cover_complex) greyblock (gudhi.plot_persistence_density parameter) (gudhi.plot_persistence_diagram parameter) grid (gudhi.tensorflow.perslay.GridPerslayWeight parameter) grid_ (gudhi.representations.vector_methods.BettiCurve attribute) (gudhi.representations.vector_methods.Entropy attribute) (gudhi.representations.vector_methods.Landscape attribute) (gudhi.representations.vector_methods.Silhouette attribute) grid_bnds (gudhi.tensorflow.perslay.GridPerslayWeight parameter) GridPerslayWeight (class in gudhi.tensorflow.perslay) gudhi.flag_filtration.edge_collapse module gudhi.point_cloud.dtm module gudhi.point_cloud.knn module gudhi.representations.kernel_methods module gudhi.representations.metrics module gudhi.representations.preprocessing module gudhi.representations.vector_methods module gudhi.subsampling module H homology_coeff_field (gudhi.CubicalComplex.compute_persistence parameter) (gudhi.CubicalComplex.persistence parameter) (gudhi.PeriodicCubicalComplex.compute_persistence parameter) (gudhi.PeriodicCubicalComplex.persistence parameter) (gudhi.SimplexTree.compute_persistence parameter) (gudhi.SimplexTree.extended_persistence parameter) (gudhi.SimplexTree.persistence parameter) (gudhi.sklearn.cubical_persistence.CubicalPersistence parameter) (gudhi.sklearn.rips_persistence.RipsPersistence parameter) (gudhi.tensorflow.CubicalLayer parameter) (gudhi.tensorflow.LowerStarSimplexTreeLayer parameter) (gudhi.tensorflow.RipsLayer parameter) homology_dimensions (gudhi.sklearn.cubical_persistence.CubicalPersistence parameter) (gudhi.sklearn.rips_persistence.RipsPersistence parameter) (gudhi.tensorflow.CubicalLayer parameter) (gudhi.tensorflow.LowerStarSimplexTreeLayer parameter) (gudhi.tensorflow.RipsLayer parameter) I im_range (gudhi.representations.vector_methods.PersistenceImage parameter) image_bnds (gudhi.tensorflow.perslay.GaussianPerslayPhi parameter) image_size (gudhi.tensorflow.perslay.GaussianPerslayPhi parameter) implementation (gudhi.point_cloud.knn.KNearestNeighbors parameter) index (gudhi.representations.preprocessing.DimensionSelector parameter) inf_delta (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_diagram parameter) init (gudhi.wasserstein.barycenter.lagrangian_barycenter parameter) initialize_filtration() (gudhi.SimplexTree method) input_edges (gudhi.flag_filtration.edge_collapse.reduce_graph parameter) input_shape (gudhi.tensorflow.perslay.FlatPerslayPhi.build parameter) (gudhi.tensorflow.perslay.GaussianMixturePerslayWeight.build parameter) (gudhi.tensorflow.perslay.GaussianPerslayPhi.build parameter) (gudhi.tensorflow.perslay.GridPerslayWeight.build parameter) (gudhi.tensorflow.perslay.Perslay.build parameter) (gudhi.tensorflow.perslay.PowerPerslayWeight.build parameter) (gudhi.tensorflow.perslay.TentPerslayPhi.build parameter) input_type (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.cover_complex.MapperComplex parameter) (gudhi.cover_complex.NerveComplex parameter) (gudhi.sklearn.cubical_persistence.CubicalPersistence parameter) (gudhi.sklearn.rips_persistence.RipsPersistence parameter) insert() (gudhi.SimplexTree method) insert_batch (gudhi.SimplexTree attribute) insert_edges_from_coo_matrix() (gudhi.SimplexTree method) internal_p (gudhi.hera.wasserstein_distance parameter) (gudhi.representations.metrics.WassersteinDistance parameter) (gudhi.wasserstein.wasserstein_distance parameter) intrisic_dim (gudhi.TangentialComplex parameter) is_empty() (gudhi.SimplexTree method) K k (gudhi.clustering.tomato.Tomato parameter) (gudhi.CoverComplex.set_color_from_coordinate parameter) (gudhi.CoverComplex.set_function_from_coordinate parameter) (gudhi.dtm_rips_complex.DTMRipsComplex parameter) (gudhi.point_cloud.dtm.DistanceToMeasure parameter) (gudhi.point_cloud.dtm.DTMDensity parameter) (gudhi.point_cloud.knn.KNearestNeighbors parameter) k_DTM (gudhi.clustering.tomato.Tomato parameter) kde_params (gudhi.clustering.tomato.Tomato parameter) keep_endpoints (gudhi.representations.vector_methods.BettiCurve parameter) (gudhi.representations.vector_methods.Entropy parameter) (gudhi.representations.vector_methods.Landscape parameter) (gudhi.representations.vector_methods.Silhouette parameter) keep_essential_parts (gudhi.wasserstein.wasserstein_distance parameter) kernel (gudhi.representations.kernel_methods.pairwise_persistence_diagram_kernels parameter) kernel_approx (gudhi.representations.kernel_methods.PersistenceFisherKernel parameter) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel parameter) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel parameter) (gudhi.representations.metrics.PersistenceFisherDistance parameter) KNearestNeighbors (class in gudhi.point_cloud.knn) kwargs (gudhi.point_cloud.dtm.DistanceToMeasure parameter) (gudhi.point_cloud.dtm.DTMDensity parameter) (gudhi.point_cloud.knn.KNearestNeighbors parameter) L labels_ (gudhi.clustering.tomato.Tomato attribute) lagrangian_barycenter() (in module gudhi.wasserstein.barycenter) landmarks (gudhi.EuclideanStrongWitnessComplex parameter) (gudhi.EuclideanWitnessComplex parameter) Landscape (class in gudhi.representations.vector_methods) leaf_labels_ (gudhi.clustering.tomato.Tomato attribute) legend (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_density parameter) (gudhi.plot_persistence_diagram parameter) limit (gudhi.representations.preprocessing.Clamping parameter) (gudhi.representations.preprocessing.DiagramSelector parameter) location (gudhi.representations.preprocessing.ProminentPoints parameter) lower_star_persistence_generators() (gudhi.SimplexTree method) LowerStarSimplexTreeLayer (class in gudhi.tensorflow) M m (gudhi.CoverComplex.set_cover_from_Voronoi parameter) make_filtration_non_decreasing() (gudhi.SimplexTree method) MapperComplex (class in gudhi.cover_complex) matching (gudhi.hera.wasserstein_distance parameter) (gudhi.wasserstein.wasserstein_distance parameter) max_alpha_square (gudhi.AlphaComplex.create_simplex_tree parameter) (gudhi.EuclideanStrongWitnessComplex.create_simplex_tree parameter) (gudhi.EuclideanWitnessComplex.create_simplex_tree parameter) (gudhi.StrongWitnessComplex.create_simplex_tree parameter) (gudhi.WitnessComplex.create_simplex_tree parameter) max_dim (gudhi.SimplexTree.expansion_with_blocker parameter) max_dimension (gudhi.RipsComplex.create_simplex_tree parameter) (gudhi.SimplexTree.expansion parameter) (gudhi.weighted_rips_complex.WeightedRipsComplex.create_simplex_tree parameter) max_edge_length (gudhi.RipsComplex parameter) max_filtration (gudhi.dtm_rips_complex.DTMRipsComplex parameter) (gudhi.SimplexTree.create_from_array parameter) (gudhi.weighted_rips_complex.WeightedRipsComplex parameter) max_intervals (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_density parameter) (gudhi.plot_persistence_diagram parameter) max_perturb (gudhi.TangentialComplex.fix_inconsistencies_using_perturbation parameter) max_squared_edge_length (gudhi.TangentialComplex.set_max_squared_edge_length parameter) max_weight_per_cc_ (gudhi.clustering.tomato.Tomato attribute) maximum_edge_length (gudhi.tensorflow.RipsLayer parameter) measure (gudhi.representations.vector_methods.Atol.__call__ parameter) merge_threshold (gudhi.clustering.tomato.Tomato parameter) merge_threshold_ (gudhi.clustering.tomato.Tomato attribute) metric (gudhi.clustering.tomato.Tomato parameter) (gudhi.point_cloud.knn.KNearestNeighbors parameter) (gudhi.representations.metrics.pairwise_persistence_diagram_distances parameter) min_dim (gudhi.SimplexTree.reset_filtration parameter) min_persistence (gudhi.CubicalComplex.compute_persistence parameter) (gudhi.CubicalComplex.persistence parameter) (gudhi.PeriodicCubicalComplex.compute_persistence parameter) (gudhi.PeriodicCubicalComplex.persistence parameter) (gudhi.SimplexTree.compute_persistence parameter) (gudhi.SimplexTree.extended_persistence parameter) (gudhi.SimplexTree.persistence parameter) (gudhi.sklearn.cubical_persistence.CubicalPersistence parameter) (gudhi.tensorflow.CubicalLayer parameter) (gudhi.tensorflow.LowerStarSimplexTreeLayer parameter) (gudhi.tensorflow.RipsLayer parameter) min_points_per_node (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.cover_complex.MapperComplex parameter) (gudhi.cover_complex.NerveComplex parameter) min_squared_dist (gudhi.subsampling.sparsify_point_set parameter) mode (gudhi.representations.metrics.WassersteinDistance parameter) (gudhi.representations.vector_methods.Entropy parameter) module gudhi.flag_filtration.edge_collapse gudhi.point_cloud.dtm gudhi.point_cloud.knn gudhi.representations.kernel_methods gudhi.representations.metrics gudhi.representations.preprocessing gudhi.representations.vector_methods gudhi.subsampling N N (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.cover_complex.MapperComplex parameter) (gudhi.cover_complex.MapperComplex.estimate_scale parameter) (gudhi.cover_complex.MapperComplex.get_optimal_parameters_for_agglomerative_clustering parameter) (gudhi.CoverComplex.compute_distribution parameter) (gudhi.CoverComplex.set_graph_from_automatic_rips parameter) n_clusters (gudhi.clustering.tomato.Tomato parameter) n_clusters_ (gudhi.clustering.tomato.Tomato attribute) n_jobs (gudhi.clustering.tomato.Tomato parameter) (gudhi.point_cloud.knn.KNearestNeighbors parameter) (gudhi.representations.kernel_methods.pairwise_persistence_diagram_kernels parameter) (gudhi.representations.kernel_methods.PersistenceFisherKernel parameter) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel parameter) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel parameter) (gudhi.representations.kernel_methods.SlicedWassersteinKernel parameter) (gudhi.representations.metrics.BottleneckDistance parameter) (gudhi.representations.metrics.pairwise_persistence_diagram_distances parameter) (gudhi.representations.metrics.PersistenceFisherDistance parameter) (gudhi.representations.metrics.SlicedWassersteinDistance parameter) (gudhi.representations.metrics.WassersteinDistance parameter) (gudhi.sklearn.cubical_persistence.CubicalPersistence parameter) (gudhi.sklearn.rips_persistence.RipsPersistence parameter) n_leaves_ (gudhi.clustering.tomato.Tomato attribute) n_samples (gudhi.datasets.generators.points.ctorus parameter) (gudhi.datasets.generators.points.sphere parameter) (gudhi.datasets.generators.points.torus parameter) (gudhi.point_cloud.dtm.DTMDensity parameter) nb_iterations (gudhi.flag_filtration.edge_collapse.reduce_graph parameter) (gudhi.SimplexTree.collapse_edges parameter) nb_points (gudhi.subsampling.choose_n_farthest_points parameter) (gudhi.subsampling.pick_n_random_points parameter) nbins (gudhi.plot_persistence_density parameter) nearest_landmark_table (gudhi.StrongWitnessComplex parameter) (gudhi.WitnessComplex parameter) NerveComplex (class in gudhi.cover_complex) nodemask (gudhi.CoverComplex.set_mask parameter) normalize (gudhi.point_cloud.dtm.DTMDensity parameter) normalized (gudhi.representations.vector_methods.Entropy parameter) num_collapses (gudhi.sklearn.rips_persistence.RipsPersistence parameter) num_directions (gudhi.representations.kernel_methods.SlicedWassersteinKernel parameter) (gudhi.representations.metrics.SlicedWassersteinDistance parameter) num_inconsistent_simplices() (gudhi.TangentialComplex method) num_inconsistent_stars() (gudhi.TangentialComplex method) num_landscapes (gudhi.representations.vector_methods.Landscape parameter) num_pts (gudhi.representations.preprocessing.ProminentPoints parameter) num_simplices() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) (gudhi.TangentialComplex method) num_vertices() (gudhi.SimplexTree method) (gudhi.TangentialComplex method) O off_file (gudhi.AlphaComplex parameter) (gudhi.CoverComplex.read_point_cloud parameter) (gudhi.read_points_from_off_file parameter) (gudhi.subsampling.choose_n_farthest_points parameter) (gudhi.subsampling.pick_n_random_points parameter) (gudhi.subsampling.sparsify_point_set parameter) (gudhi.TangentialComplex parameter) only_this_dim (gudhi.read_persistence_intervals_in_dimension parameter) order (gudhi.hera.wasserstein_distance parameter) (gudhi.representations.metrics.WassersteinDistance parameter) (gudhi.wasserstein.wasserstein_distance parameter) other (gudhi.SimplexTree parameter) P p (gudhi.clustering.tomato.Tomato parameter) (gudhi.point_cloud.knn.KNearestNeighbors parameter) Padding (class in gudhi.representations.preprocessing) pairwise_persistence_diagram_distances() (in module gudhi.representations.metrics) pairwise_persistence_diagram_kernels() (in module gudhi.representations.kernel_methods) params (gudhi.clustering.tomato.Tomato parameter) params_ (gudhi.clustering.tomato.Tomato attribute) pdiagset (gudhi.wasserstein.barycenter.lagrangian_barycenter parameter) periodic_dimensions (gudhi.PeriodicCubicalComplex parameter), [1], [2], [3] PeriodicCubicalComplex (class in gudhi) perm_op (gudhi.tensorflow.perslay.Perslay parameter) perseus_file (gudhi.CubicalComplex parameter) (gudhi.PeriodicCubicalComplex parameter) persistence (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_density parameter) (gudhi.plot_persistence_diagram parameter) persistence() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) persistence_dim_max (gudhi.SimplexTree.compute_persistence parameter) (gudhi.SimplexTree.persistence parameter) (gudhi.tensorflow.LowerStarSimplexTreeLayer parameter) persistence_file (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_density parameter) (gudhi.plot_persistence_diagram parameter) (gudhi.read_persistence_intervals_grouped_by_dimension parameter) (gudhi.read_persistence_intervals_in_dimension parameter) (gudhi.SimplexTree.write_persistence_diagram parameter) persistence_intervals_in_dimension() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) persistence_pairs() (gudhi.SimplexTree method) PersistenceFisherDistance (class in gudhi.representations.metrics) PersistenceFisherKernel (class in gudhi.representations.kernel_methods) PersistenceImage (class in gudhi.representations.vector_methods) PersistenceScaleSpaceKernel (class in gudhi.representations.kernel_methods) PersistenceWeightedGaussianKernel (class in gudhi.representations.kernel_methods) persistent_betti_numbers() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) Perslay (class in gudhi.tensorflow.perslay) phi (gudhi.tensorflow.perslay.Perslay parameter) pick_n_random_points() (in module gudhi.subsampling) plot_diagram() (gudhi.clustering.tomato.Tomato method) plot_dot() (gudhi.CoverComplex method) plot_off() (gudhi.CoverComplex method) plot_persistence_barcode() (in module gudhi) plot_persistence_density() (in module gudhi) plot_persistence_diagram() (in module gudhi) point_type (gudhi.representations.preprocessing.DiagramSelector parameter) points (gudhi.AlphaComplex parameter) (gudhi.dtm_rips_complex.DTMRipsComplex parameter) (gudhi.RipsComplex parameter) (gudhi.subsampling.choose_n_farthest_points parameter) (gudhi.subsampling.pick_n_random_points parameter) (gudhi.subsampling.sparsify_point_set parameter) (gudhi.TangentialComplex parameter) (gudhi.write_points_to_off_file parameter) polynomial_type (gudhi.representations.vector_methods.ComplexPolynomial parameter) power (gudhi.CoverComplex.set_subsampling parameter) (gudhi.tensorflow.perslay.PowerPerslayWeight parameter) PowerPerslayWeight (class in gudhi.tensorflow.perslay) precision (gudhi.AlphaComplex parameter) (gudhi.AlphaComplex.set_float_relative_precision parameter) predefined_grid (gudhi.representations.vector_methods.BettiCurve parameter) ProminentPoints (class in gudhi.representations.preprocessing) prune_above_dimension() (gudhi.SimplexTree method) prune_above_filtration() (gudhi.SimplexTree method) Q q (gudhi.clustering.tomato.Tomato parameter) (gudhi.dtm_rips_complex.DTMRipsComplex parameter) (gudhi.point_cloud.dtm.DistanceToMeasure parameter) (gudhi.point_cloud.dtm.DTMDensity parameter) quantiser (gudhi.representations.vector_methods.Atol parameter) R r (gudhi.clustering.tomato.Tomato parameter) radius (gudhi.datasets.generators.points.sphere parameter) read_lower_triangular_matrix_from_csv_file() (in module gudhi) read_persistence_intervals_grouped_by_dimension() (in module gudhi) read_persistence_intervals_in_dimension() (in module gudhi) read_point_cloud() (gudhi.CoverComplex method) read_points_from_off_file() (in module gudhi) reduce_graph() (in module gudhi.flag_filtration.edge_collapse) remove_maximal_simplex() (gudhi.SimplexTree method) reset_filtration() (gudhi.SimplexTree method) resolution (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.CoverComplex.set_resolution_with_interval_length parameter) (gudhi.CoverComplex.set_resolution_with_interval_number parameter) (gudhi.representations.vector_methods.BettiCurve parameter) (gudhi.representations.vector_methods.Entropy parameter) (gudhi.representations.vector_methods.Landscape parameter) (gudhi.representations.vector_methods.PersistenceImage parameter) (gudhi.representations.vector_methods.Silhouette parameter) resolutions (gudhi.cover_complex.MapperComplex parameter) return_distance (gudhi.point_cloud.knn.KNearestNeighbors parameter) return_index (gudhi.point_cloud.knn.KNearestNeighbors parameter) rho (gudhi.tensorflow.perslay.Perslay parameter) rips_threshold (gudhi.cover_complex.GraphInducedComplex parameter) RipsComplex (class in gudhi) RipsLayer (class in gudhi.tensorflow) RipsPersistence (class in gudhi.sklearn.rips_persistence) S sample (gudhi.datasets.generators.points.ctorus parameter) (gudhi.datasets.generators.points.sphere parameter) (gudhi.datasets.generators.points.torus parameter) sample_range (gudhi.representations.vector_methods.BettiCurve parameter) (gudhi.representations.vector_methods.Entropy parameter) (gudhi.representations.vector_methods.Landscape parameter) (gudhi.representations.vector_methods.Silhouette parameter) sample_weight (gudhi.representations.vector_methods.Atol.fit parameter) (gudhi.representations.vector_methods.Atol.set_fit_request parameter) (gudhi.representations.vector_methods.Atol.set_transform_request parameter) (gudhi.representations.vector_methods.Atol.transform parameter) samples (gudhi.tensorflow.perslay.FlatPerslayPhi parameter) (gudhi.tensorflow.perslay.TentPerslayPhi parameter) save_to_dot() (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) save_to_html() (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) save_to_txt() (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) scalers (gudhi.representations.preprocessing.DiagramScaler parameter) separator (gudhi.read_lower_triangular_matrix_from_csv_file parameter) set_attributes_from_colors (gudhi.cover_complex.GraphInducedComplex.get_networkx parameter) (gudhi.cover_complex.MapperComplex.get_networkx parameter) (gudhi.cover_complex.NerveComplex.get_networkx parameter) set_automatic_resolution() (gudhi.CoverComplex method) set_color_from_coordinate() (gudhi.CoverComplex method) set_color_from_file() (gudhi.CoverComplex method) set_color_from_range() (gudhi.CoverComplex method) set_cover_from_file() (gudhi.CoverComplex method) set_cover_from_function() (gudhi.CoverComplex method) set_cover_from_range() (gudhi.CoverComplex method) set_cover_from_Voronoi() (gudhi.CoverComplex method) set_dimension() (gudhi.SimplexTree method) set_distances_from_range() (gudhi.CoverComplex method) set_fit_request() (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) (gudhi.representations.vector_methods.Atol method) set_float_relative_precision() (gudhi.AlphaComplex static method) set_function_from_coordinate() (gudhi.CoverComplex method) set_function_from_file() (gudhi.CoverComplex method) set_function_from_range() (gudhi.CoverComplex method) set_gain() (gudhi.CoverComplex method) set_graph_from_automatic_rips() (gudhi.CoverComplex method) set_graph_from_file() (gudhi.CoverComplex method) set_graph_from_OFF() (gudhi.CoverComplex method) set_graph_from_rips() (gudhi.CoverComplex method) set_mask() (gudhi.CoverComplex method) set_max_squared_edge_length() (gudhi.TangentialComplex method) set_params() (gudhi.cover_complex.GraphInducedComplex method) (gudhi.cover_complex.MapperComplex method) (gudhi.cover_complex.NerveComplex method) set_point_cloud_from_range() (gudhi.CoverComplex method) set_resolution_with_interval_length() (gudhi.CoverComplex method) set_resolution_with_interval_number() (gudhi.CoverComplex method) set_subsampling() (gudhi.CoverComplex method) set_transform_request() (gudhi.representations.vector_methods.Atol method) set_type() (gudhi.CoverComplex method) set_verbose() (gudhi.CoverComplex method) Silhouette (class in gudhi.representations.vector_methods) simplex (gudhi.SimplexTree.assign_filtration parameter) (gudhi.SimplexTree.filtration parameter) (gudhi.SimplexTree.find parameter) (gudhi.SimplexTree.get_boundaries parameter) (gudhi.SimplexTree.get_cofaces parameter) (gudhi.SimplexTree.get_star parameter) (gudhi.SimplexTree.insert parameter) (gudhi.SimplexTree.remove_maximal_simplex parameter) SimplexTree (class in gudhi) simplextree (gudhi.tensorflow.LowerStarSimplexTreeLayer parameter) skip (gudhi.point_cloud.timedelay.TimeDelayEmbedding parameter) SlicedWassersteinDistance (class in gudhi.representations.metrics) SlicedWassersteinKernel (class in gudhi.representations.kernel_methods) sort_results (gudhi.point_cloud.knn.KNearestNeighbors parameter) sparse (gudhi.RipsComplex parameter) sparsify_point_set() (in module gudhi.subsampling) sphere() (in module gudhi.datasets.generators.points) starting_point (gudhi.subsampling.choose_n_farthest_points parameter) state (gudhi.SimplexTree.__setstate__ parameter) StrongWitnessComplex (class in gudhi) subcolor() (gudhi.CoverComplex method) subpopulation() (gudhi.CoverComplex method) subset (gudhi.datasets.remote.fetch_daily_activities parameter) symmetrize_graph (gudhi.clustering.tomato.Tomato parameter) T TangentialComplex (class in gudhi) TentPerslayPhi (class in gudhi.tensorflow.perslay) theta (gudhi.tensorflow.perslay.FlatPerslayPhi parameter) threshold (gudhi.CoverComplex.set_graph_from_rips parameter) (gudhi.representations.preprocessing.ProminentPoints parameter) (gudhi.representations.vector_methods.ComplexPolynomial parameter) (gudhi.representations.vector_methods.TopologicalVector parameter) (gudhi.sklearn.rips_persistence.RipsPersistence parameter) time_limit (gudhi.TangentialComplex.fix_inconsistencies_using_perturbation parameter) TimeDelayEmbedding (class in gudhi.point_cloud.timedelay) to_value (gudhi.CubicalComplex.persistent_betti_numbers parameter) (gudhi.PeriodicCubicalComplex.persistent_betti_numbers parameter) (gudhi.SimplexTree.persistent_betti_numbers parameter) Tomato (class in gudhi.clustering.tomato) top_dimensional_cells (gudhi.CubicalComplex parameter), [1] (gudhi.PeriodicCubicalComplex parameter), [1] top_dimensional_cells() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) TopologicalVector (class in gudhi.representations.vector_methods) torus() (in module gudhi.datasets.generators.points) transform() (gudhi.point_cloud.dtm.DistanceToMeasure method) (gudhi.point_cloud.dtm.DTMDensity method) (gudhi.point_cloud.knn.KNearestNeighbors method) (gudhi.point_cloud.timedelay.TimeDelayEmbedding method) (gudhi.representations.kernel_methods.PersistenceFisherKernel method) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel method) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel method) (gudhi.representations.kernel_methods.SlicedWassersteinKernel method) (gudhi.representations.metrics.BottleneckDistance method) (gudhi.representations.metrics.PersistenceFisherDistance method) (gudhi.representations.metrics.SlicedWassersteinDistance method) (gudhi.representations.metrics.WassersteinDistance method) (gudhi.representations.preprocessing.BirthPersistenceTransform method) (gudhi.representations.preprocessing.Clamping method) (gudhi.representations.preprocessing.DiagramScaler method) (gudhi.representations.preprocessing.DiagramSelector method) (gudhi.representations.preprocessing.DimensionSelector method) (gudhi.representations.preprocessing.Padding method) (gudhi.representations.preprocessing.ProminentPoints method) (gudhi.representations.vector_methods.Atol method) (gudhi.representations.vector_methods.BettiCurve method) (gudhi.representations.vector_methods.ComplexPolynomial method) (gudhi.representations.vector_methods.Entropy method) (gudhi.representations.vector_methods.Landscape method) (gudhi.representations.vector_methods.PersistenceImage method) (gudhi.representations.vector_methods.Silhouette method) (gudhi.representations.vector_methods.TopologicalVector method) (gudhi.sklearn.cubical_persistence.CubicalPersistence method) (gudhi.sklearn.rips_persistence.RipsPersistence method) ts (gudhi.point_cloud.timedelay.TimeDelayEmbedding.__call__ parameter) (gudhi.point_cloud.timedelay.TimeDelayEmbedding.transform parameter) type (gudhi.CoverComplex.set_type parameter) U upper_bound_dimension() (gudhi.SimplexTree method) use (gudhi.representations.preprocessing.DiagramScaler parameter) (gudhi.representations.preprocessing.DiagramSelector parameter) (gudhi.representations.preprocessing.Padding parameter) (gudhi.representations.preprocessing.ProminentPoints parameter) V variance (gudhi.tensorflow.perslay.GaussianPerslayPhi parameter) verbose (gudhi.cover_complex.GraphInducedComplex parameter) (gudhi.cover_complex.MapperComplex parameter) (gudhi.cover_complex.NerveComplex parameter) (gudhi.CoverComplex.set_verbose parameter) (gudhi.wasserstein.barycenter.lagrangian_barycenter parameter) vertex (gudhi.AlphaComplex.get_point parameter) (gudhi.EuclideanStrongWitnessComplex.get_point parameter) (gudhi.EuclideanWitnessComplex.get_point parameter) (gudhi.TangentialComplex.get_point parameter) vertices (gudhi.CubicalComplex parameter), [1] (gudhi.PeriodicCubicalComplex parameter), [1] vertices() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) vertices_of_persistence_pairs() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) voronoi_samples (gudhi.cover_complex.GraphInducedComplex parameter) W wasserstein_distance() (in module gudhi.hera) (in module gudhi.wasserstein) WassersteinDistance (class in gudhi.representations.metrics) weight (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel parameter) (gudhi.representations.vector_methods.PersistenceImage parameter) (gudhi.representations.vector_methods.Silhouette parameter) (gudhi.tensorflow.perslay.Perslay parameter) WeightedRipsComplex (class in gudhi.weighted_rips_complex) weighting_method (gudhi.representations.vector_methods.Atol parameter) weights (gudhi.AlphaComplex parameter) (gudhi.clustering.tomato.Tomato.fit parameter) (gudhi.point_cloud.dtm.DTMDensity parameter) (gudhi.weighted_rips_complex.WeightedRipsComplex parameter) weights_ (gudhi.clustering.tomato.Tomato attribute) WitnessComplex (class in gudhi) witnesses (gudhi.EuclideanStrongWitnessComplex parameter) (gudhi.EuclideanWitnessComplex parameter) write_info() (gudhi.CoverComplex method) write_persistence_diagram() (gudhi.SimplexTree method) write_points_to_off_file() (in module gudhi) X X (gudhi.clustering.tomato.Tomato.fit parameter) (gudhi.cover_complex.GraphInducedComplex.fit parameter) (gudhi.cover_complex.MapperComplex.estimate_scale parameter) (gudhi.cover_complex.MapperComplex.fit parameter) (gudhi.cover_complex.MapperComplex.get_optimal_parameters_for_agglomerative_clustering parameter) (gudhi.cover_complex.NerveComplex.fit parameter) (gudhi.hera.bottleneck_distance parameter) (gudhi.hera.wasserstein_distance parameter) (gudhi.point_cloud.dtm.DistanceToMeasure.fit parameter) (gudhi.point_cloud.dtm.DistanceToMeasure.transform parameter) (gudhi.point_cloud.dtm.DTMDensity.fit parameter) (gudhi.point_cloud.dtm.DTMDensity.transform parameter) (gudhi.point_cloud.knn.KNearestNeighbors.fit parameter) (gudhi.point_cloud.knn.KNearestNeighbors.transform parameter) (gudhi.representations.kernel_methods.pairwise_persistence_diagram_kernels parameter) (gudhi.representations.kernel_methods.PersistenceFisherKernel.fit parameter) (gudhi.representations.kernel_methods.PersistenceFisherKernel.transform parameter) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel.fit parameter) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel.transform parameter) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel.fit parameter) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel.transform parameter) (gudhi.representations.kernel_methods.SlicedWassersteinKernel.fit parameter) (gudhi.representations.kernel_methods.SlicedWassersteinKernel.transform parameter) (gudhi.representations.metrics.BottleneckDistance.fit parameter) (gudhi.representations.metrics.BottleneckDistance.transform parameter) (gudhi.representations.metrics.pairwise_persistence_diagram_distances parameter) (gudhi.representations.metrics.PersistenceFisherDistance.fit parameter) (gudhi.representations.metrics.PersistenceFisherDistance.transform parameter) (gudhi.representations.metrics.SlicedWassersteinDistance.fit parameter) (gudhi.representations.metrics.SlicedWassersteinDistance.transform parameter) (gudhi.representations.metrics.WassersteinDistance.fit parameter) (gudhi.representations.metrics.WassersteinDistance.transform parameter) (gudhi.representations.preprocessing.BirthPersistenceTransform.fit parameter) (gudhi.representations.preprocessing.BirthPersistenceTransform.transform parameter) (gudhi.representations.preprocessing.Clamping.fit parameter) (gudhi.representations.preprocessing.Clamping.transform parameter) (gudhi.representations.preprocessing.DiagramScaler.fit parameter) (gudhi.representations.preprocessing.DiagramScaler.transform parameter) (gudhi.representations.preprocessing.DiagramSelector.fit parameter) (gudhi.representations.preprocessing.DiagramSelector.transform parameter) (gudhi.representations.preprocessing.DimensionSelector.transform parameter) (gudhi.representations.preprocessing.Padding.fit parameter) (gudhi.representations.preprocessing.Padding.transform parameter) (gudhi.representations.preprocessing.ProminentPoints.fit parameter) (gudhi.representations.preprocessing.ProminentPoints.transform parameter) (gudhi.representations.vector_methods.Atol.fit parameter) (gudhi.representations.vector_methods.Atol.transform parameter) (gudhi.representations.vector_methods.BettiCurve.fit parameter) (gudhi.representations.vector_methods.BettiCurve.transform parameter) (gudhi.representations.vector_methods.ComplexPolynomial.fit parameter) (gudhi.representations.vector_methods.ComplexPolynomial.transform parameter) (gudhi.representations.vector_methods.Entropy.fit parameter) (gudhi.representations.vector_methods.Entropy.transform parameter) (gudhi.representations.vector_methods.Landscape.fit parameter) (gudhi.representations.vector_methods.Landscape.transform parameter) (gudhi.representations.vector_methods.PersistenceImage.fit parameter) (gudhi.representations.vector_methods.PersistenceImage.transform parameter) (gudhi.representations.vector_methods.Silhouette.fit parameter) (gudhi.representations.vector_methods.Silhouette.transform parameter) (gudhi.representations.vector_methods.TopologicalVector.fit parameter) (gudhi.representations.vector_methods.TopologicalVector.transform parameter) (gudhi.sklearn.cubical_persistence.CubicalPersistence.transform parameter) (gudhi.sklearn.rips_persistence.RipsPersistence.transform parameter) (gudhi.tensorflow.CubicalLayer.call parameter) (gudhi.tensorflow.RipsLayer.call parameter) (gudhi.wasserstein.wasserstein_distance parameter) Y y (gudhi.clustering.tomato.Tomato.fit parameter) (gudhi.cover_complex.GraphInducedComplex.fit parameter) (gudhi.cover_complex.MapperComplex.fit parameter) (gudhi.cover_complex.NerveComplex.fit parameter) Y (gudhi.hera.bottleneck_distance parameter) (gudhi.hera.wasserstein_distance parameter) (gudhi.representations.kernel_methods.pairwise_persistence_diagram_kernels parameter) y (gudhi.representations.kernel_methods.PersistenceFisherKernel.fit parameter) (gudhi.representations.kernel_methods.PersistenceScaleSpaceKernel.fit parameter) (gudhi.representations.kernel_methods.PersistenceWeightedGaussianKernel.fit parameter) (gudhi.representations.kernel_methods.SlicedWassersteinKernel.fit parameter) (gudhi.representations.metrics.BottleneckDistance.fit parameter) Y (gudhi.representations.metrics.pairwise_persistence_diagram_distances parameter) y (gudhi.representations.metrics.PersistenceFisherDistance.fit parameter) (gudhi.representations.metrics.SlicedWassersteinDistance.fit parameter) (gudhi.representations.metrics.WassersteinDistance.fit parameter) (gudhi.representations.preprocessing.BirthPersistenceTransform.fit parameter) (gudhi.representations.preprocessing.Clamping.fit parameter) (gudhi.representations.preprocessing.DiagramScaler.fit parameter) (gudhi.representations.preprocessing.DiagramSelector.fit parameter) (gudhi.representations.preprocessing.Padding.fit parameter) (gudhi.representations.preprocessing.ProminentPoints.fit parameter) (gudhi.representations.vector_methods.Atol.fit parameter) (gudhi.representations.vector_methods.BettiCurve.fit parameter) (gudhi.representations.vector_methods.ComplexPolynomial.fit parameter) (gudhi.representations.vector_methods.Entropy.fit parameter) (gudhi.representations.vector_methods.Landscape.fit parameter) (gudhi.representations.vector_methods.PersistenceImage.fit parameter) (gudhi.representations.vector_methods.Silhouette.fit parameter) (gudhi.representations.vector_methods.TopologicalVector.fit parameter) Y (gudhi.wasserstein.wasserstein_distance parameter)
