Index

_

__init__() (mesh_tools.meshlab.Decimator method) (mesh_tools.meshlab.FillHoles method) (mesh_tools.meshlab.FilterBase method) (mesh_tools.meshlab.Interior method) (mesh_tools.meshlab.Meshlab method) (mesh_tools.meshlab.Poisson method) (mesh_tools.meshlab.Scripter method)

A

accuracy_stats_from_true_predicted_skeleton() (in module mesh_tools.skeleton_utils) add_and_smooth_segment_to_branch() (in module mesh_tools.skeleton_utils) add_filters() (mesh_tools.meshlab.Scripter method) add_params() (mesh_tools.meshlab.Scripter method)

adjust_param() (mesh_tools.meshlab.Scripter method) align_skeletons_at_connectivity() (in module mesh_tools.skeleton_utils) angle_between_skeleton_vectors_and_ref_vector() (in module mesh_tools.skeleton_utils) area() (in module mesh_tools.trimesh_utils) area_of_vertex_boundary() (in module mesh_tools.trimesh_utils)

B

bbox() (in module mesh_tools.skeleton_utils) bbox_intersect_test() (in module mesh_tools.trimesh_utils) bbox_max_x() (in module mesh_tools.trimesh_utils) bbox_max_y() (in module mesh_tools.trimesh_utils) bbox_max_z() (in module mesh_tools.trimesh_utils) bbox_mesh() (in module mesh_tools.trimesh_utils) bbox_mesh_restriction() (in module mesh_tools.trimesh_utils) bbox_min_x() (in module mesh_tools.trimesh_utils) bbox_min_y() (in module mesh_tools.trimesh_utils) bbox_min_z() (in module mesh_tools.trimesh_utils) bbox_side_length_ratios() (in module mesh_tools.trimesh_utils) bbox_volume() (in module mesh_tools.skeleton_utils) (in module mesh_tools.trimesh_utils)

bbox_volume_oriented() (in module mesh_tools.trimesh_utils) border_euclidean_length() (in module mesh_tools.trimesh_utils) bounding_box() (in module mesh_tools.trimesh_utils) bounding_box_center() (in module mesh_tools.trimesh_utils) bounding_box_corner_max() (in module mesh_tools.trimesh_utils) bounding_box_corner_min() (in module mesh_tools.trimesh_utils) bounding_box_corners() (in module mesh_tools.skeleton_utils) (in module mesh_tools.trimesh_utils) bounding_box_longest_side() (in module mesh_tools.trimesh_utils) bounding_box_oriented_side_lengths() (in module mesh_tools.trimesh_utils) box_mesh() (in module mesh_tools.trimesh_utils) branches_from_mesh() (in module mesh_tools.meshparty_skeletonize)

C

calcification() (in module mesh_tools.skeleton_utils) calculate_coordinate_distances_cumsum() (in module mesh_tools.skeleton_utils) calculate_skeletal_distance() (in module mesh_tools.skeleton_utils) calculate_skeletal_length() (in module mesh_tools.skeleton_utils) calculate_skeleton_distance() (in module mesh_tools.skeleton_utils) calculate_skeleton_paths_on_mesh() (in module mesh_tools.meshparty_skeletonize) calculate_skeleton_segment_distances() (in module mesh_tools.skeleton_utils) center_at_origin() (in module mesh_tools.trimesh_utils) center_mesh() (in module mesh_tools.trimesh_utils) center_mesh_at_point() (in module mesh_tools.trimesh_utils) center_skeleton() (in module mesh_tools.skeleton_utils) centered_at_origin() (in module mesh_tools.trimesh_utils) change_basis_matrix() (in module mesh_tools.skeleton_utils) check_coordinates_inside_bounding_box() (in module mesh_tools.trimesh_utils) check_correspondence_branches_have_2_endpoints() (in module mesh_tools.skeleton_utils) check_meshes_inside_mesh_bbox() (in module mesh_tools.trimesh_utils) check_meshes_inside_multiple_mesh_bbox() (in module mesh_tools.trimesh_utils) check_meshes_outside_mesh_bbox() (in module mesh_tools.trimesh_utils) check_meshes_outside_multiple_mesh_bbox() (in module mesh_tools.trimesh_utils) check_skeleton_connected_component() (in module mesh_tools.skeleton_utils) check_skeleton_one_component() (in module mesh_tools.skeleton_utils) clean_skeleton() (in module mesh_tools.skeleton_utils) clean_skeleton_with_decompose() (in module mesh_tools.skeleton_utils) clean_skeleton_with_soma_verts() (in module mesh_tools.skeleton_utils) clear_meshlab_port() (in module mesh_tools.meshlab) close_hole_area_max() (in module mesh_tools.trimesh_utils) close_hole_area_top_2_mean() (in module mesh_tools.trimesh_utils) close_hole_area_top_k_extrema() (in module mesh_tools.trimesh_utils) close_hole_areas() (in module mesh_tools.trimesh_utils) close_mesh_holes() (in module mesh_tools.trimesh_utils) close_mesh_holes_at_vertices() (in module mesh_tools.trimesh_utils) closest_connected_component_mesh_to_coordinates() (in module mesh_tools.trimesh_utils) closest_coordinate_to_mesh_faces() (in module mesh_tools.trimesh_utils) closest_distance_between_meshes() (in module mesh_tools.trimesh_utils) closest_distances_from_skeleton_vertices_to_base_skeleton() (in module mesh_tools.skeleton_utils) closest_face_to_coordinate() (in module mesh_tools.trimesh_utils) closest_face_to_coordinate_distance() (in module mesh_tools.trimesh_utils) closest_face_to_coordinates() (in module mesh_tools.trimesh_utils) closest_face_to_mesh_center_distance() (in module mesh_tools.trimesh_utils) closest_mesh_attribute_to_coordinates_fast() (in module mesh_tools.trimesh_utils) closest_mesh_coordinate_to_other_mesh() (in module mesh_tools.trimesh_utils) closest_mesh_distance_to_coordinates_fast() (in module mesh_tools.trimesh_utils) closest_mesh_to_coordinate() (in module mesh_tools.trimesh_utils) closest_mesh_to_coordinates() (in module mesh_tools.trimesh_utils) closest_mesh_to_mesh() (in module mesh_tools.trimesh_utils) closest_mesh_vertex_to_other_mesh() (in module mesh_tools.trimesh_utils) closest_n_attributes_to_coordinate() (in module mesh_tools.trimesh_utils)

closest_segmentation_to_coordinate() (in module mesh_tools.trimesh_utils) closest_skeleton_coordinate() (in module mesh_tools.skeleton_utils) closest_skeleton_coordinates() (in module mesh_tools.skeleton_utils) closest_split_to_coordinate() (in module mesh_tools.trimesh_utils) collapse_soma_skeleton() (in module mesh_tools.meshparty_skeletonize) combine_close_branch_points() (in module mesh_tools.skeleton_utils) combine_dicts() (mesh_tools.meshlab.Scripter static method) combine_meshes() (in module mesh_tools.trimesh_utils) compare_endpoints() (in module mesh_tools.skeleton_utils) compare_meshes_by_face_midpoints() (in module mesh_tools.trimesh_utils) compare_meshes_by_face_midpoints_list() (in module mesh_tools.trimesh_utils) compare_skeletons_ordered() (in module mesh_tools.skeleton_utils) components_to_submeshes() (in module mesh_tools.trimesh_utils) compute_segments() (in module mesh_tools.meshparty_skeletonize) connected_component_meshes() (in module mesh_tools.trimesh_utils) connected_components_from_face_idx() (in module mesh_tools.trimesh_utils) connected_components_from_mesh() (in module mesh_tools.trimesh_utils) connected_nondegenerate_mesh() (in module mesh_tools.trimesh_utils) convert_branch_graph_to_skeleton() (in module mesh_tools.skeleton_utils) convert_graph_to_skeleton() (in module mesh_tools.skeleton_utils) convert_meshes_to_face_idxes() (in module mesh_tools.trimesh_utils) convert_nodes_edges_to_skeleton() (in module mesh_tools.skeleton_utils) convert_o3d_to_trimesh() (in module mesh_tools.trimesh_utils) convert_skeleton_to_coordinates() (in module mesh_tools.skeleton_utils) convert_skeleton_to_graph() (in module mesh_tools.skeleton_utils) convert_skeleton_to_graph_old() (in module mesh_tools.skeleton_utils) convert_skeleton_to_nodes() (in module mesh_tools.skeleton_utils) convert_skeleton_to_nodes_edges() (in module mesh_tools.skeleton_utils) convert_skeleton_to_nodes_edges_old() (in module mesh_tools.skeleton_utils) convert_skeleton_to_nodes_edges_optimized() (in module mesh_tools.skeleton_utils) convert_skeleton_to_nodes_edges_optimized_old() (in module mesh_tools.skeleton_utils) convert_trimesh_to_o3d() (in module mesh_tools.trimesh_utils) coordinate_on_mesh_mesh_border() (in module mesh_tools.trimesh_utils) coordinate_restriction_to_skeleton() (in module mesh_tools.skeleton_utils) coordinates_along_skeleton_offset_from_start() (in module mesh_tools.skeleton_utils) coordinates_from_downstream_dist() (in module mesh_tools.skeleton_utils) coordinates_to_bounding_box() (in module mesh_tools.trimesh_utils) coordinates_to_enclosing_sphere() (in module mesh_tools.trimesh_utils) coordinates_to_enclosing_sphere_center_radius() (in module mesh_tools.trimesh_utils) coordinates_to_enclosing_sphere_volume() (in module mesh_tools.trimesh_utils) correspondence_1_to_1() (in module mesh_tools.correspondence_utils) create_decimation_script() (mesh_tools.meshlab.Decimator class method) create_filter() (mesh_tools.meshlab.Scripter static method) create_filter_script() (mesh_tools.meshlab.FilterBase method) create_param() (mesh_tools.meshlab.Scripter static method) create_poisson_script() (mesh_tools.meshlab.Poisson class method) create_soma_extending_branches() (in module mesh_tools.skeleton_utils) cut_skeleton_at_coordinate() (in module mesh_tools.skeleton_utils)

D

decimate() (in module mesh_tools.trimesh_utils) Decimator (class in mesh_tools.meshlab) decompose_skeleton_to_branches() (in module mesh_tools.skeleton_utils) default_mesh_stats_to_run() (in module mesh_tools.trimesh_utils)

delete_filter() (mesh_tools.meshlab.Scripter method) delete_param() (mesh_tools.meshlab.Scripter method) divide_branch() (in module mesh_tools.skeleton_utils) divide_mesh_into_connected_components() (in module mesh_tools.trimesh_utils) downsample_skeleton() (in module mesh_tools.skeleton_utils)

E

empty_mesh() (in module mesh_tools.trimesh_utils) empty_skeleton() (in module mesh_tools.skeleton_utils) endpoint_connectivity() (in module mesh_tools.skeleton_utils)

example_cgal_skeletonization_original_params() (in module mesh_tools.skeleton_utils) expand_border_faces() (in module mesh_tools.trimesh_utils) export_mesh() (in module mesh_tools.trimesh_utils)

F

face_idx_map_from_face_idx_list() (in module mesh_tools.trimesh_utils) face_midpoints_x_z() (in module mesh_tools.trimesh_utils) face_neighbors_by_vertices() (in module mesh_tools.trimesh_utils) face_neighbors_by_vertices_seperate() (in module mesh_tools.trimesh_utils) faces_closer_than_distance_of_coordinates() (in module mesh_tools.trimesh_utils) faces_defined_by_vertices_idx_list_to_mesh() (in module mesh_tools.trimesh_utils) faces_farther_than_distance_of_coordinates() (in module mesh_tools.trimesh_utils) farthest_coordinate_to_faces() (in module mesh_tools.trimesh_utils) farthest_face_to_coordinate() (in module mesh_tools.trimesh_utils) farthest_face_to_coordinate_distance() (in module mesh_tools.trimesh_utils) farthest_face_to_mesh_center_distance() (in module mesh_tools.trimesh_utils) fetch_mesh_from_off() (mesh_tools.meshlab.Meshlab static method) fill_holes() (in module mesh_tools.trimesh_utils) fill_holes_trimesh() (in module mesh_tools.trimesh_utils) fill_mesh_holes() (in module mesh_tools.trimesh_utils) fill_mesh_holes_with_fan() (in module mesh_tools.trimesh_utils) fill_single_triangle_holes() (in module mesh_tools.trimesh_utils) FillHoles (class in mesh_tools.meshlab) filter_away_border_touching_submeshes_by_group() (in module mesh_tools.trimesh_utils) filter_away_connected_comp_in_face_idx_with_minimum_vertex_distance_to_coordinates() (in module mesh_tools.trimesh_utils) filter_away_inside_meshes() (in module mesh_tools.trimesh_utils) filter_away_leaf_skeletons() (in module mesh_tools.skeleton_utils)

filter_away_small_skeleton_offshoots() (in module mesh_tools.skeleton_utils) filter_face_coloring_to_connected_components() (in module mesh_tools.compartment_utils) filter_meshes_by_bounding_box_longest_side() (in module mesh_tools.trimesh_utils) filter_meshes_by_containing_coordinates() (in module mesh_tools.trimesh_utils) filter_meshes_by_size() (in module mesh_tools.trimesh_utils) filter_meshes_by_size_min_max() (in module mesh_tools.trimesh_utils) filter_vertices_by_mesh() (in module mesh_tools.trimesh_utils) FilterBase (class in mesh_tools.meshlab) filters (mesh_tools.meshlab.Scripter property) find_border_face_groups() (in module mesh_tools.trimesh_utils) find_border_faces() (in module mesh_tools.trimesh_utils) find_border_vertex_groups() (in module mesh_tools.trimesh_utils) find_border_vertices() (in module mesh_tools.trimesh_utils) find_branch_endpoints() (in module mesh_tools.skeleton_utils) find_branch_skeleton_with_specific_coordinate() (in module mesh_tools.skeleton_utils) find_closest_coordinate_to_mesh_faces() (in module mesh_tools.trimesh_utils) find_closest_face_to_coordinates() (in module mesh_tools.trimesh_utils) find_degenerate_faces() (in module mesh_tools.trimesh_utils) find_end_nodes_with_significant_mesh_correspondence() (in module mesh_tools.skeleton_utils) find_large_dense_submesh() (in module mesh_tools.trimesh_utils) find_nondegenerate_faces() (in module mesh_tools.trimesh_utils) find_skeleton_endpoint_coordinates() (in module mesh_tools.skeleton_utils) flip_skeleton() (in module mesh_tools.skeleton_utils)

G

generate_surface_skeleton() (in module mesh_tools.skeleton_utils) generate_surface_skeleton_slower() (in module mesh_tools.skeleton_utils) get_non_manifold_edges() (in module mesh_tools.trimesh_utils) get_non_manifold_vertices() (in module mesh_tools.trimesh_utils) get_ordered_branch_nodes_coordinates() (in module mesh_tools.skeleton_utils)

get_skeletal_distance() (in module mesh_tools.compartment_utils) get_skeletal_distance_no_skipping() (in module mesh_tools.compartment_utils) gram_schmidt_columns() (in module mesh_tools.skeleton_utils) graph_skeleton_and_mesh() (in module mesh_tools.skeleton_utils) groups_of_labels_to_resolved_labels() (in module mesh_tools.compartment_utils)

H

high_degree_coordinates_on_path() (in module mesh_tools.skeleton_utils)

high_degree_coordinates_on_skeleton() (in module mesh_tools.skeleton_utils)

I

initialize_script_filters() (mesh_tools.meshlab.Decimator static method) (mesh_tools.meshlab.FillHoles method) (mesh_tools.meshlab.Interior method) (mesh_tools.meshlab.Poisson static method) Interior (class in mesh_tools.meshlab) interpercentile_range_face_midpoints() (in module mesh_tools.trimesh_utils) interpercentile_range_face_midpoints_volume() (in module mesh_tools.trimesh_utils) interpercentile_range_face_midpoints_x() (in module mesh_tools.trimesh_utils) interpercentile_range_face_midpoints_y() (in module mesh_tools.trimesh_utils)

interpercentile_range_face_midpoints_z() (in module mesh_tools.trimesh_utils) intersect_skeleton() (in module mesh_tools.skeleton_utils) ipr_first_second_largest_eigenvector_xz_diff() (in module mesh_tools.trimesh_utils) ipr_largest_eigenvector_xy() (in module mesh_tools.trimesh_utils) ipr_largest_eigenvector_xz() (in module mesh_tools.trimesh_utils) ipr_second_largest_eigenvector_xz() (in module mesh_tools.trimesh_utils) is_manifold() (in module mesh_tools.trimesh_utils) is_mesh() (in module mesh_tools.trimesh_utils) is_watertight() (in module mesh_tools.trimesh_utils)

J

jitter_skeleton_from_coordinate() (in module mesh_tools.skeleton_utils)

K

kd_tree_from_unique_coordinates() (in module mesh_tools.skeleton_utils)

kdtree_length() (in module mesh_tools.trimesh_utils)

L

largest_border_to_coordinate() (in module mesh_tools.trimesh_utils) largest_conn_comp() (in module mesh_tools.trimesh_utils) largest_hole_length() (in module mesh_tools.trimesh_utils)

list_len_measure() (in module mesh_tools.skeleton_utils) load_mesh_no_processing() (in module mesh_tools.trimesh_utils) load_mesh_no_processing_h5() (in module mesh_tools.trimesh_utils)

M

map_between_branches_lists() (in module mesh_tools.skeleton_utils) map_between_branches_lists_old() (in module mesh_tools.skeleton_utils) matching_endpoint_singular() (in module mesh_tools.skeleton_utils) matching_skeleton_branches_by_endpoints() (in module mesh_tools.skeleton_utils) matching_skeleton_branches_by_vertices() (in module mesh_tools.skeleton_utils) max_distance_betwee_mesh_vertices() (in module mesh_tools.trimesh_utils) mesh_bbox_contains_skeleton() (in module mesh_tools.trimesh_utils) mesh_center_vertex_average() (in module mesh_tools.trimesh_utils) mesh_center_weighted_face_midpoints() (in module mesh_tools.trimesh_utils) mesh_centered_at_origin() (in module mesh_tools.trimesh_utils) mesh_correspondence_adaptive_distance() (in module mesh_tools.compartment_utils) mesh_correspondence_first_pass() (in module mesh_tools.correspondence_utils) mesh_face_graph_by_vertex() (in module mesh_tools.trimesh_utils) mesh_from_vertices_faces() (in module mesh_tools.trimesh_utils) mesh_interior() (in module mesh_tools.trimesh_utils) mesh_kdtree_face() (in module mesh_tools.trimesh_utils) mesh_kdtree_vertices() (in module mesh_tools.trimesh_utils) mesh_list_connectivity() (in module mesh_tools.trimesh_utils) mesh_list_distance_connectivity() (in module mesh_tools.trimesh_utils) mesh_overlap_with_restriction_mesh() (in module mesh_tools.trimesh_utils) mesh_pieces_connectivity() (in module mesh_tools.trimesh_utils) mesh_restriction_to_skeleton() (in module mesh_tools.skeleton_utils) mesh_segmentation() (in module mesh_tools.trimesh_utils) mesh_segmentation_from_skeleton() (in module mesh_tools.trimesh_utils) mesh_segmentation_largest_conn_comp() (in module mesh_tools.trimesh_utils) mesh_size() (in module mesh_tools.trimesh_utils) mesh_stats() (in module mesh_tools.trimesh_utils) mesh_subtraction_by_skeleton() (in module mesh_tools.skeleton_utils) mesh_subtraction_by_skeleton_old() (in module mesh_tools.skeleton_utils) mesh_teasar() (in module mesh_tools.meshparty_skeletonize) mesh_to_kdtree() (in module mesh_tools.trimesh_utils) mesh_to_off() (mesh_tools.meshlab.Meshlab static method) mesh_tools module

mesh_tools.compartment_utils module mesh_tools.correspondence_utils module mesh_tools.meshlab module mesh_tools.meshparty_skeletonize module mesh_tools.skeleton_utils module mesh_tools.trimesh_utils module mesh_vertex_graph() (in module mesh_tools.trimesh_utils) mesh_volume() (in module mesh_tools.trimesh_utils) mesh_volume_convex_hull() (in module mesh_tools.trimesh_utils) mesh_volume_o3d() (in module mesh_tools.trimesh_utils) mesh_volume_ratio() (in module mesh_tools.trimesh_utils) mesh_with_ends_cutoff() (in module mesh_tools.trimesh_utils) meshes_distance_matrix() (in module mesh_tools.trimesh_utils) meshes_within_close_proximity() (in module mesh_tools.trimesh_utils) Meshlab (class in mesh_tools.meshlab) min_cut_to_partition_mesh_vertices() (in module mesh_tools.trimesh_utils) mls_buffer (mesh_tools.meshlab.Scripter property) module mesh_tools mesh_tools.compartment_utils mesh_tools.correspondence_utils mesh_tools.meshlab mesh_tools.meshparty_skeletonize mesh_tools.skeleton_utils mesh_tools.trimesh_utils move_point_to_nearest_branch_end_point_within_threshold() (in module mesh_tools.skeleton_utils)

N

n_faces() (in module mesh_tools.trimesh_utils) n_vertices_inside_mesh_bbox() (in module mesh_tools.trimesh_utils) n_vertices_outside_mesh_bbox() (in module mesh_tools.trimesh_utils)

node_names_and_coord_from_G() (in module mesh_tools.skeleton_utils) number_connected_components() (in module mesh_tools.skeleton_utils) number_connected_components_branches() (in module mesh_tools.skeleton_utils)

O

offset_skeletons_aligned_at_shared_endpoint() (in module mesh_tools.skeleton_utils) offset_skeletons_aligned_parent_child_skeletal_angle() (in module mesh_tools.skeleton_utils) old_combine_close_branch_points() (in module mesh_tools.skeleton_utils) order_resize_skeleton() (in module mesh_tools.skeleton_utils) order_skeleton() (in module mesh_tools.skeleton_utils) order_skeletons_connecting_endpoints() (in module mesh_tools.skeleton_utils)

original_mesh_faces_map() (in module mesh_tools.trimesh_utils) original_mesh_vertices_map() (in module mesh_tools.trimesh_utils) overlapping_attribute() (in module mesh_tools.trimesh_utils) overlapping_faces() (in module mesh_tools.trimesh_utils) overlapping_vertices() (in module mesh_tools.trimesh_utils) overlapping_vertices_from_face_lists() (in module mesh_tools.trimesh_utils)

P

parent_child_skeletal_angle() (in module mesh_tools.skeleton_utils) path_ordered_skeleton() (in module mesh_tools.skeleton_utils) percentage_skeleton_match_to_ref_vector() (in module mesh_tools.skeleton_utils) percentage_vertices_inside() (in module mesh_tools.trimesh_utils) plot_correspondence() (in module mesh_tools.correspondence_utils) plot_correspondence_on_single_mesh() (in module mesh_tools.correspondence_utils) plot_ipv_mesh() (in module mesh_tools.skeleton_utils) plot_ipv_scatter() (in module mesh_tools.skeleton_utils)

plot_ipv_skeleton() (in module mesh_tools.skeleton_utils) plot_segmentation() (in module mesh_tools.trimesh_utils) Poisson (class in mesh_tools.meshlab) poisson_surface_reconstruction() (in module mesh_tools.trimesh_utils) preprocessing() (mesh_tools.meshlab.Decimator class method) (mesh_tools.meshlab.FilterBase method) (mesh_tools.meshlab.Poisson class method) pymeshfix_clean() (in module mesh_tools.trimesh_utils)

Q

query_meshes_from_restrictions() (in module mesh_tools.trimesh_utils)

query_meshes_from_stats() (in module mesh_tools.trimesh_utils)

R

radius_sphere_from_volume() (in module mesh_tools.trimesh_utils) ratio_closest_face_to_mesh_center_distance_to_width() (in module mesh_tools.trimesh_utils) ratio_farthest_face_to_mesh_center_distance_to_width() (in module mesh_tools.trimesh_utils) ratio_ipr_eigenvector_xz_diff_to_width() (in module mesh_tools.trimesh_utils) ratio_mesh_stat_to_width() (in module mesh_tools.trimesh_utils) ray_trace_distance() (in module mesh_tools.meshparty_skeletonize) (in module mesh_tools.trimesh_utils) ray_trace_distance_by_mesh_center_dist() (in module mesh_tools.trimesh_utils) read_skeleton_edges_coordinates() (in module mesh_tools.skeleton_utils) read_skeleton_verts_edges() (in module mesh_tools.skeleton_utils) recompose_skeleton_from_branches() (in module mesh_tools.skeleton_utils) reduce_verts() (in module mesh_tools.meshparty_skeletonize) remove_cycles_from_skeleton() (in module mesh_tools.skeleton_utils)

remove_degenerate_faces() (in module mesh_tools.trimesh_utils) remove_mesh_interior() (in module mesh_tools.trimesh_utils) resize_and_center_skeleton() (in module mesh_tools.skeleton_utils) resize_center_and_coordinates_from_skeleton() (in module mesh_tools.skeleton_utils) resize_skeleton_branch() (in module mesh_tools.skeleton_utils) resize_skeleton_with_branching() (in module mesh_tools.skeleton_utils) resolve_empty_conflicting_face_labels() (in module mesh_tools.compartment_utils) restrict_mesh() (in module mesh_tools.trimesh_utils) restrict_mesh_list_by_mesh() (in module mesh_tools.trimesh_utils) restrict_meshes_from_stats() (in module mesh_tools.trimesh_utils) restrict_skeleton_from_start() (in module mesh_tools.skeleton_utils) restrict_skeleton_from_start_plus_offset() (in module mesh_tools.skeleton_utils) restrict_skeleton_to_distance_from_coordinate() (in module mesh_tools.skeleton_utils) rotate_mesh_from_matrix() (in module mesh_tools.trimesh_utils)

S

save_skeleton_cgal() (in module mesh_tools.skeleton_utils) scatter_mesh_with_radius() (in module mesh_tools.trimesh_utils) Scripter (class in mesh_tools.meshlab) set_filter() (mesh_tools.meshlab.Scripter method) set_meshlab_port() (in module mesh_tools.meshlab) set_param() (mesh_tools.meshlab.Scripter method) setdiff_skeleton() (in module mesh_tools.skeleton_utils) setup_root() (in module mesh_tools.meshparty_skeletonize) (in module mesh_tools.skeleton_utils) shared_coordiantes() (in module mesh_tools.skeleton_utils) shared_edges_between_faces_on_mesh() (in module mesh_tools.trimesh_utils) shared_endpoint() (in module mesh_tools.skeleton_utils) shortest_path_between_two_sets_of_skeleton_coordiantes() (in module mesh_tools.skeleton_utils) skeletal_distance() (in module mesh_tools.skeleton_utils) skeletal_length_from_mesh() (in module mesh_tools.trimesh_utils) skeleton_and_mesh_segmentation() (in module mesh_tools.trimesh_utils) skeleton_cgal() (in module mesh_tools.skeleton_utils) skeleton_cgal_original_parameters() (in module mesh_tools.skeleton_utils) skeleton_connected_components() (in module mesh_tools.skeleton_utils) skeleton_coordinate_offset_from_endpoint() (in module mesh_tools.skeleton_utils) skeleton_coordinate_path_from_start() (in module mesh_tools.skeleton_utils) skeleton_endpoint_vector() (in module mesh_tools.skeleton_utils) skeleton_from_h5py() (in module mesh_tools.skeleton_utils) skeleton_graph_nodes_to_group() (in module mesh_tools.skeleton_utils) skeleton_list_connectivity() (in module mesh_tools.skeleton_utils) skeleton_list_connectivity_slow() (in module mesh_tools.skeleton_utils) skeleton_n_components() (in module mesh_tools.skeleton_utils) skeleton_non_branching_from_mesh() (in module mesh_tools.trimesh_utils) skeleton_obj_to_branches() (in module mesh_tools.meshparty_skeletonize) skeleton_path_between_skeleton_coordinates() (in module mesh_tools.skeleton_utils) skeleton_to_mesh_correspondence() (in module mesh_tools.trimesh_utils) skeleton_unique_coordinates() (in module mesh_tools.skeleton_utils) skeleton_vectors() (in module mesh_tools.skeleton_utils) skeletonize() (in module mesh_tools.meshparty_skeletonize)

skeletonize_and_clean_connected_branch_CGAL() (in module mesh_tools.skeleton_utils) skeletonize_components() (in module mesh_tools.meshparty_skeletonize) skeletonize_connected_branch() (in module mesh_tools.skeleton_utils) skeletonize_connected_branch_meshparty() (in module mesh_tools.skeleton_utils) skeletonize_mesh() (in module mesh_tools.meshparty_skeletonize) skeletonize_mesh_largest_component() (in module mesh_tools.meshparty_skeletonize) skelton_coordinate_path_to_skeleton() (in module mesh_tools.skeleton_utils) smooth_graph() (in module mesh_tools.meshparty_skeletonize) smooth_skeleton_branch() (in module mesh_tools.skeleton_utils) soma_skeleton_stitching() (in module mesh_tools.skeleton_utils) sort_meshes_largest_to_smallest() (in module mesh_tools.trimesh_utils) sphere_mesh() (in module mesh_tools.trimesh_utils) split() (in module mesh_tools.trimesh_utils) split_by_vertices() (in module mesh_tools.trimesh_utils) split_mesh_by_closest_skeleton() (in module mesh_tools.trimesh_utils) split_mesh_into_face_groups() (in module mesh_tools.trimesh_utils) split_significant_pieces() (in module mesh_tools.trimesh_utils) split_significant_pieces_old() (in module mesh_tools.trimesh_utils) split_skeleton_into_edges() (in module mesh_tools.skeleton_utils) split_vertex_list_into_connected_components() (in module mesh_tools.trimesh_utils) split_vertex_list_into_connected_components_old() (in module mesh_tools.trimesh_utils) stack_skeletons() (in module mesh_tools.skeleton_utils) stats_df() (in module mesh_tools.trimesh_utils) stitch() (in module mesh_tools.trimesh_utils) stitch_mesh_at_vertices() (in module mesh_tools.trimesh_utils) stitch_mesh_holes() (in module mesh_tools.trimesh_utils) stitch_skeleton() (in module mesh_tools.skeleton_utils) submesh() (in module mesh_tools.trimesh_utils) subskeleton_from_vertices_idx() (in module mesh_tools.skeleton_utils) subtract_exact_coordinates_from_skeleton() (in module mesh_tools.skeleton_utils) subtract_mesh() (in module mesh_tools.trimesh_utils) surface_area() (in module mesh_tools.trimesh_utils) surface_area_to_volume() (in module mesh_tools.trimesh_utils) surface_skeleton() (in module mesh_tools.skeleton_utils)

T

test_filters() (mesh_tools.meshlab.Scripter method) test_inside_meshes() (in module mesh_tools.trimesh_utils) to_file() (mesh_tools.meshlab.Scripter method)

translate_mesh() (in module mesh_tools.trimesh_utils) turn_off_logging() (in module mesh_tools.trimesh_utils) two_mesh_list_connectivity() (in module mesh_tools.trimesh_utils)

U

unique_port (mesh_tools.meshlab.Meshlab attribute)

V

valid_coordiantes_mapped_to_mesh() (in module mesh_tools.trimesh_utils) vector_away_from_endpoint() (in module mesh_tools.skeleton_utils) vertex_components() (in module mesh_tools.trimesh_utils) vertex_indices_subgraph() (in module mesh_tools.trimesh_utils) vertices_coordinates_to_faces() (in module mesh_tools.trimesh_utils)

vertices_coordinates_to_faces_old() (in module mesh_tools.trimesh_utils) vertices_coordinates_to_vertex_index() (in module mesh_tools.trimesh_utils) vertices_mask_inside_mesh_bbox() (in module mesh_tools.trimesh_utils) vertices_mask_inside_meshes_bbox() (in module mesh_tools.trimesh_utils) vertices_to_faces() (in module mesh_tools.trimesh_utils)

W

waterfill_labeling() (in module mesh_tools.compartment_utils) waterfill_starting_label_to_soma_border() (in module mesh_tools.compartment_utils) waterfilling_face_idx() (in module mesh_tools.trimesh_utils) width_median_weighted() (in module mesh_tools.meshparty_skeletonize) width_of_submesh() (in module mesh_tools.trimesh_utils) width_ray() (in module mesh_tools.trimesh_utils)

width_ray_trace_median() (in module mesh_tools.trimesh_utils) width_ray_trace_perc() (in module mesh_tools.trimesh_utils) width_ray_trace_perc_of_submesh() (in module mesh_tools.trimesh_utils) widths_of_submeshes() (in module mesh_tools.trimesh_utils) write_h5_file() (in module mesh_tools.trimesh_utils) write_neuron_off() (in module mesh_tools.trimesh_utils)