Index

Symbols

**kwargs (gudhi.representations.kernel_methods.pairwise_persistence_diagram_kernels parameter) (gudhi.representations.metrics.pairwise_persistence_diagram_distances 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) __init__() (gudhi.AlphaComplex method) (gudhi.clustering.tomato.Tomato 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.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.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.StrongWitnessComplex method) (gudhi.TangentialComplex method) (gudhi.weighted_rips_complex.WeightedRipsComplex method) (gudhi.WitnessComplex method)

A

alpha (gudhi.CoverComplex.compute_distance_from_confidence_level parameter) (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_diagram parameter) AlphaComplex (class in gudhi)

assign_filtration() (gudhi.SimplexTree method) 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)

betti_numbers() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) BettiCurve (class in gudhi.representations.vector_methods) BirthPersistenceTransform (class in gudhi.representations.preprocessing) bottleneck_distance() (in module gudhi) (in module gudhi.hera) BottleneckDistance (class in gudhi.representations.metrics) bw_method (gudhi.plot_persistence_density parameter)

C

c (gudhi.CoverComplex.subpopulation parameter) children_ (gudhi.clustering.tomato.Tomato attribute) choose_n_farthest_points() (in module gudhi.subsampling) Clamping (class in gudhi.representations.preprocessing) cloud (gudhi.CoverComplex.set_point_cloud_from_range 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.CoverComplex.set_color_from_range parameter) color_file_name (gudhi.CoverComplex.set_color_from_file parameter) colormap (gudhi.plot_persistence_barcode parameter) (gudhi.plot_persistence_diagram 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) contrast (gudhi.representations.vector_methods.Atol parameter) cover_file_name (gudhi.CoverComplex.set_cover_from_file parameter) CoverComplex (class in gudhi) 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) CubicalComplex (class in gudhi)

D

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.BettiCurve.__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) DiagramScaler (class in gudhi.representations.preprocessing) DiagramSelector (class in gudhi.representations.preprocessing) dim (gudhi.clustering.tomato.Tomato 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.set_dimension parameter) dimension() (gudhi.CubicalComplex method) (gudhi.PeriodicCubicalComplex method) (gudhi.SimplexTree method) dimensions (gudhi.CubicalComplex parameter) (gudhi.PeriodicCubicalComplex parameter) 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) 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)

epsilon (gudhi.representations.metrics.BottleneckDistance parameter) EuclideanStrongWitnessComplex (class in gudhi) EuclideanWitnessComplex (class in gudhi) expansion() (gudhi.SimplexTree method) extend_filtration() (gudhi.SimplexTree method) extended_persistence() (gudhi.SimplexTree method)

F

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) find() (gudhi.SimplexTree method) find_simplices() (gudhi.CoverComplex method) fit() (gudhi.clustering.tomato.Tomato 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.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)

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) fix_inconsistencies_using_perturbation() (gudhi.TangentialComplex method) flag_persistence_generators() (gudhi.SimplexTree method) 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) get_boundaries() (gudhi.SimplexTree method) get_cofaces() (gudhi.SimplexTree method) get_filtration() (gudhi.SimplexTree 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_file_name (gudhi.CoverComplex.set_graph_from_file parameter) graph_type (gudhi.clustering.tomato.Tomato parameter) greyblock (gudhi.plot_persistence_density parameter) (gudhi.plot_persistence_diagram parameter) 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)

I

im_range (gudhi.representations.vector_methods.PersistenceImage parameter) implementation (gudhi.point_cloud.knn.KNearestNeighbors 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) insert() (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)

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)

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)

M

m (gudhi.CoverComplex.set_cover_from_Voronoi parameter) make_filtration_non_decreasing() (gudhi.SimplexTree method) matching (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 parameter) max_dimension (gudhi.RipsComplex.create_simplex_tree 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.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) 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) min_squared_dist (gudhi.subsampling.sparsify_point_set parameter) mode (gudhi.representations.metrics.WassersteinDistance parameter) (gudhi.representations.vector_methods.Entropy parameter)

N

N (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) n_leaves_ (gudhi.clustering.tomato.Tomato attribute) n_samples (gudhi.point_cloud.dtm.DTMDensity parameter) nb_iterations (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) nodemask (gudhi.CoverComplex.set_mask parameter) normalize (gudhi.point_cloud.dtm.DTMDensity parameter) normalized (gudhi.representations.vector_methods.Entropy 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)

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] PeriodicCubicalComplex (class in gudhi) 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) 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) 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) polynomial_type (gudhi.representations.vector_methods.ComplexPolynomial parameter) power (gudhi.CoverComplex.set_subsampling parameter) precision (gudhi.AlphaComplex parameter) ProminentPoints (class in gudhi.representations.preprocessing) 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) 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) remove_maximal_simplex() (gudhi.SimplexTree method) reset_filtration() (gudhi.SimplexTree method) resolution (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)

return_distance (gudhi.point_cloud.knn.KNearestNeighbors parameter) return_index (gudhi.point_cloud.knn.KNearestNeighbors parameter) RipsComplex (class in gudhi)

S

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.transform parameter) scalers (gudhi.representations.preprocessing.DiagramScaler parameter) separator (gudhi.read_lower_triangular_matrix_from_csv_file 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_Voronoi() (gudhi.CoverComplex method) set_dimension() (gudhi.SimplexTree method) set_distances_from_range() (gudhi.CoverComplex 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_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_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) 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) starting_point (gudhi.subsampling.choose_n_farthest_points parameter) StrongWitnessComplex (class in gudhi) subpopulation() (gudhi.CoverComplex method) symmetrize_graph (gudhi.clustering.tomato.Tomato parameter)

T

TangentialComplex (class in gudhi) 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) 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] TopologicalVector (class in gudhi.representations.vector_methods) 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.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)

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

verbose (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)

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) WeightedRipsComplex (class in gudhi.weighted_rips_complex) weighting_method (gudhi.representations.vector_methods.Atol parameter)

weights (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)

X

X (gudhi.clustering.tomato.Tomato.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.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.wasserstein.wasserstein_distance parameter)

Y

y (gudhi.clustering.tomato.Tomato.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)