Index

_

__init__() (query method) (query_container method)

A

add_dissimilarity_weight_to_edges() (in module muspan.networks) (in module muspan.networks.add_dissimilarity_weight_to_edges) add_labels() (domain method) add_lines() (domain method) add_objects_to_collection() (domain method) add_points() (domain method) add_query() (query_container method), [1] add_shapes() (domain method) add_shapes_with_internal_holes() (domain method) add_similarity_weight_to_edges() (in module muspan.networks) (in module muspan.networks.add_similarity_weight_to_edges)

adjacency_permutation_test() (in module muspan.networks) (in module muspan.networks.adjacency_permutation_test) alpha_index() (in module muspan.networks) (in module muspan.networks.alpha_index) alpha_shape() (in module muspan.helpers), [1] are_points_clockwise_oriented() (in module muspan.shape_operations.helpers) (in module muspan.shape_operations.helpers.are_points_clockwise_oriented) area() (in module muspan.geometry) (in module muspan.geometry.area) average_nearest_neighbour_index() (in module muspan.spatial_statistics), [1]

B

barcode() (in module muspan.visualise) (in module muspan.visualise.barcode)

C

centrality() (in module muspan.networks) change_some_elements() (in module muspan.spatial_statistics.helpers.change_some_elements) circularity() (in module muspan.geometry) (in module muspan.geometry.circularity) clean_up() (in module muspan.helpers) cluster_data() (in module muspan.helpers), [1] cluster_neighbourhoods() (in module muspan.networks) (in module muspan.networks.cluster_neighbourhoods) combine_include_and_exclude_boundaries() (in module muspan.helpers), [1] combine_shapes() (in module muspan.shape_operations), [1] community_detection() (in module muspan.networks) (in module muspan.networks.community_detection) compactness() (in module muspan.networks) (in module muspan.networks.compactness)

convert_objects() (domain method) convexity() (in module muspan.geometry) (in module muspan.geometry.convexity) coords_to_poly() (in module muspan.shape_operations.helpers.get_union_of_set_of_shapes) (in module muspan.shape_operations.helpers.return_difference_of_shapes_from_boundaries) (in module muspan.shape_operations.helpers.return_intersection_of_shapes_from_boundaries) crop_domain() (in module muspan.helpers) cross_k_function() (in module muspan.spatial_statistics), [1] cross_l_function() (in module muspan.spatial_statistics), [1] cross_pair_correlation_function() (in module muspan.spatial_statistics), [1] cyclomatic_number() (in module muspan.networks) (in module muspan.networks.cyclomatic_number)

D

delete_distances() (domain method) delete_labels() (domain method) delete_network() (domain method) delete_objects() (domain method) distance_point_to_line_segment() (in module muspan.shape_operations.helpers) (in module muspan.shape_operations.helpers.distance_point_to_line_segment), [1]

distance_point_to_polygon() (in module muspan.shape_operations.helpers.distance_point_to_polygon) distance_polygon_to_polygon() (in module muspan.shape_operations.helpers.distance_polygon_to_polygon) do_polygons_intersect() (in module muspan.shape_operations.helpers.do_polygons_intersect) do_shapes_intersect() (in module muspan.shape_operations.helpers.do_shapes_intersect) domain (class in muspan) domain_to_csv() (in module muspan.io)

E

edge_orientation_distribution() (in module muspan.networks) (in module muspan.networks.edge_orientation_distribution)

estimate_boundary() (domain method)

F

filter_objects_to_included_regions() (in module muspan.query) find_a_subtraction_region_from_starting_point() (in module muspan.shape_operations.helpers.get_polygon_subtraction_regions)

find_a_union_region_from_starting_point() (in module muspan.shape_operations.helpers.get_polygon_union_regions) find_an_intersection_region_from_starting_point() (in module muspan.shape_operations.helpers.get_polygon_intersection_regions) find_line_intersections_2D() (in module muspan.shape_operations.helpers.find_line_intersections_2D)

G

gamma_index() (in module muspan.networks) (in module muspan.networks.gamma_index) generate_distribution() (in module muspan.distribution), [1] (in module muspan.distribution.generate_distribution) generate_hexgrid() (in module muspan.region_based), [1] generate_network() (in module muspan.networks) (in module muspan.networks.generate_network) generate_quadrats() (in module muspan.region_based), [1] get_area() (in module muspan.shape_operations.helpers.get_polygon_intersection_regions) get_c_from_sigma_inv() (in module muspan.spatial_statistics.helpers.get_c_from_sigma_inv) get_candidates_from_merging_newpair_into_list() (in module muspan.shape_operations.helpers.get_polygon_intersection_points) get_centroids() (in module muspan.query), [1] get_children() (in module muspan.query), [1] get_collections() (in module muspan.query), [1] get_family_tree() (in module muspan.query), [1]

get_intersection_area_circle_and_polygon() (in module muspan.shape_operations.helpers.get_intersection_area_circle_and_polygon) get_labels() (in module muspan.query), [1] get_minimum_distances_boundaries() (in module muspan.query), [1] get_minimum_distances_centroids() (in module muspan.query), [1] get_object_components() (in module muspan.query), [1] get_object_types() (in module muspan.query), [1] get_parents() (in module muspan.query), [1] get_polygon_intersection_points() (in module muspan.shape_operations.helpers.get_polygon_intersection_points) get_polygon_intersection_regions() (in module muspan.shape_operations.helpers.get_polygon_intersection_regions) get_polygon_subtraction_regions() (in module muspan.shape_operations.helpers.get_polygon_subtraction_regions) get_polygon_union_regions() (in module muspan.shape_operations.helpers.get_polygon_union_regions) get_subcomponent_coords_from_component_ID() (in module muspan.helpers), [1] get_union_of_set_of_shapes() (in module muspan.shape_operations.helpers.get_union_of_set_of_shapes) getis_ord() (in module muspan.spatial_statistics) (in module muspan.spatial_statistics.getis_ord)

I

interpret_query() (in module muspan.query), [1]

is_A_contained_by_B() (in module muspan.query), [1] is_query_like() (in module muspan.query), [1]

J

J_function() (in module muspan.spatial_statistics)

K

kernel_density_estimation() (in module muspan.distribution), [1] (in module muspan.distribution.kernel_density_estimation) khop_neighbourhood() (in module muspan.networks) (in module muspan.networks.khop_neighbourhood)

kl_divergence() (in module muspan.distribution) (in module muspan.distribution.kl_divergence) knn_label_count() (in module muspan.networks) (in module muspan.networks.knn_label_count)

L

label_counts() (in module muspan.summary_statistics), [1] (in module muspan.summary_statistics.label_counts) label_density() (in module muspan.summary_statistics), [1] (in module muspan.summary_statistics.label_density) label_entropy() (in module muspan.summary_statistics) (in module muspan.summary_statistics.label_entropy)

level_set_filtration() (in module muspan.topology) (in module muspan.topology.level_set_filtration) Line (class in muspan.objects) load_domain() (in module muspan.io) (in module muspan.io.load_domain) load_example_domain() (in module muspan.datasets), [1] (in module muspan.datasets.load_example_domain)

M

module muspan.datasets.load_example_domain muspan.helpers.object_to_shape_distance_matrix muspan.shape_operations.helpers muspan.shape_operations.helpers.are_points_clockwise_oriented muspan.shape_operations.helpers.distance_point_to_line_segment muspan.shape_operations.helpers.distance_point_to_polygon muspan.shape_operations.helpers.distance_polygon_to_polygon muspan.shape_operations.helpers.do_polygons_intersect muspan.shape_operations.helpers.do_shapes_intersect muspan.shape_operations.helpers.find_line_intersections_2D muspan.shape_operations.helpers.get_intersection_area_circle_and_polygon muspan.shape_operations.helpers.get_polygon_intersection_points muspan.shape_operations.helpers.get_polygon_intersection_regions muspan.shape_operations.helpers.get_polygon_subtraction_regions muspan.shape_operations.helpers.get_polygon_union_regions muspan.shape_operations.helpers.get_union_of_set_of_shapes muspan.shape_operations.helpers.point_in_polygon muspan.shape_operations.helpers.polygon_in_polygon muspan.shape_operations.helpers.remove_zero_length_polygon_edges muspan.shape_operations.helpers.return_difference_of_shapes_from_boundaries muspan.shape_operations.helpers.return_intersection_of_shapes_from_boundaries muspan.shape_operations.helpers.return_union_of_shapes_from_boundaries muspan.spatial_statistics.helpers muspan.spatial_statistics.helpers.change_some_elements muspan.spatial_statistics.helpers.get_c_from_sigma_inv morans_i() (in module muspan.spatial_statistics) (in module muspan.spatial_statistics.morans_i) morisita_horn_index() (in module muspan.region_based) muspan.datasets.load_example_domain module muspan.helpers.object_to_shape_distance_matrix module muspan.shape_operations.helpers module muspan.shape_operations.helpers.are_points_clockwise_oriented module muspan.shape_operations.helpers.distance_point_to_line_segment module

muspan.shape_operations.helpers.distance_point_to_polygon module muspan.shape_operations.helpers.distance_polygon_to_polygon module muspan.shape_operations.helpers.do_polygons_intersect module muspan.shape_operations.helpers.do_shapes_intersect module muspan.shape_operations.helpers.find_line_intersections_2D module muspan.shape_operations.helpers.get_intersection_area_circle_and_polygon module muspan.shape_operations.helpers.get_polygon_intersection_points module muspan.shape_operations.helpers.get_polygon_intersection_regions module muspan.shape_operations.helpers.get_polygon_subtraction_regions module muspan.shape_operations.helpers.get_polygon_union_regions module muspan.shape_operations.helpers.get_union_of_set_of_shapes module muspan.shape_operations.helpers.point_in_polygon module muspan.shape_operations.helpers.polygon_in_polygon module muspan.shape_operations.helpers.remove_zero_length_polygon_edges module muspan.shape_operations.helpers.return_difference_of_shapes_from_boundaries module muspan.shape_operations.helpers.return_intersection_of_shapes_from_boundaries module muspan.shape_operations.helpers.return_union_of_shapes_from_boundaries module muspan.spatial_statistics.helpers module muspan.spatial_statistics.helpers.change_some_elements module muspan.spatial_statistics.helpers.get_c_from_sigma_inv module

N

nearest_neighbour_distribution() (in module muspan.spatial_statistics) network_distance() (in module muspan.networks) (in module muspan.networks.network_distance)

node_degree() (in module muspan.networks) (in module muspan.networks.node_degree)

O

object_to_object_distance_matrix() (in module muspan.helpers), [1]

object_to_shape_distance_matrix() (in module muspan.helpers)

P

perimeter() (in module muspan.geometry) (in module muspan.geometry.perimeter) persistence_diagram() (in module muspan.visualise) (in module muspan.visualise.persistence_diagram) persistence_image() (in module muspan.visualise) (in module muspan.visualise.persistence_image)

Point (class in muspan.objects) point_in_polygon() (in module muspan.shape_operations.helpers.point_in_polygon) polygon_in_polygon() (in module muspan.shape_operations.helpers.polygon_in_polygon) principle_axis() (in module muspan.geometry) (in module muspan.geometry.principle_axis) print_collections() (domain method) print_labels() (domain method)

Q

quadrat_correlation_matrix() (in module muspan.region_based), [1] query (class in muspan.query), [1]

query_container (class in muspan.query), [1] qupath_to_domain() (in module muspan.io)

R

remove_zero_length_polygon_edges() (in module muspan.shape_operations.helpers.remove_zero_length_polygon_edges) return_difference_of_shapes() (in module muspan.shape_operations), [1] return_difference_of_shapes_from_boundaries() (in module muspan.shape_operations.helpers.return_difference_of_shapes_from_boundaries) return_intersection_of_shapes() (in module muspan.shape_operations), [1]

return_intersection_of_shapes_from_boundaries() (in module muspan.shape_operations.helpers.return_intersection_of_shapes_from_boundaries) return_object_IDs_from_query_like() (in module muspan.query) return_union_of_shapes() (in module muspan.shape_operations), [1] return_union_of_shapes_from_boundaries() (in module muspan.shape_operations.helpers.return_union_of_shapes_from_boundaries)

S

save_domain() (in module muspan.io) (in module muspan.io.save_domain) Shape (class in muspan.objects) signed_triangle_area_times_2() (in module muspan.shape_operations.helpers.find_line_intersections_2D) simplify_shape_boundaries() (domain method) sliced_wasserstein_distance() (in module muspan.distribution), [1] (in module muspan.distribution.sliced_wasserstein_distance)

spatialdata_to_domain() (in module muspan.io) (in module muspan.io.spatialdata_to_domain) spherical_contact_distribution() (in module muspan.spatial_statistics) summarise_distribution() (in module muspan.distribution) (in module muspan.distribution.summarise_distribution)

T

topographical_correlation_map() (in module muspan.spatial_statistics), [1]

triplet_orientation() (in module muspan.shape_operations.helpers.find_line_intersections_2D)

U

update_colors() (domain method)

V

validate_query() (in module muspan.query), [1] vectorise_persistence() (in module muspan.topology) (in module muspan.topology.vectorise_persistence) vietoris_rips_filtration() (in module muspan.topology) (in module muspan.topology.vietoris_rips_filtration) visualise() (in module muspan.visualise) (in module muspan.visualise.visualise) visualise_correlation_matrix() (in module muspan.visualise) (in module muspan.visualise.visualise_correlation_matrix)

visualise_family_tree() (in module muspan.visualise) (in module muspan.visualise.visualise_family_tree) visualise_heatmap() (in module muspan.visualise) visualise_network() (in module muspan.visualise) (in module muspan.visualise.visualise_network) visualise_spatial_statistic() (in module muspan.visualise) visualise_topographical_correlation_map() (in module muspan.visualise) (in module muspan.visualise.visualise_topographical_correlation_map) visualise_wpcf() (in module muspan.visualise) (in module muspan.visualise.visualise_wpcf)

W

weighted_pair_correlation_function() (in module muspan.spatial_statistics), [1]

X

xenium_to_domain() (in module muspan.io) (in module muspan.io.xenium_to_domain)