mesh_tools

• mesh_tools package
  • Submodules
  • mesh_tools.compartment_utils module
    • filter_face_coloring_to_connected_components()
    • get_skeletal_distance()
    • get_skeletal_distance_no_skipping()
    • groups_of_labels_to_resolved_labels()
    • mesh_correspondence_adaptive_distance()
    • resolve_empty_conflicting_face_labels()
    • waterfill_labeling()
    • waterfill_starting_label_to_soma_border()
  • mesh_tools.correspondence_utils module
    • correspondence_1_to_1()
    • mesh_correspondence_first_pass()
    • plot_correspondence()
    • plot_correspondence_on_single_mesh()
  • mesh_tools.meshlab module
    • Decimator
      • Decimator.__init__()
      • Decimator.create_decimation_script()
      • Decimator.initialize_script_filters()
      • Decimator.preprocessing()
    • FillHoles
      • FillHoles.__init__()
      • FillHoles.initialize_script_filters()
    • FilterBase
      • FilterBase.__init__()
      • FilterBase.create_filter_script()
      • FilterBase.preprocessing()
    • Interior
      • Interior.__init__()
      • Interior.initialize_script_filters()
    • Meshlab
      • Meshlab.__init__()
      • Meshlab.fetch_mesh_from_off()
      • Meshlab.mesh_to_off()
      • Meshlab.unique_port
    • Poisson
      • Poisson.__init__()
      • Poisson.create_poisson_script()
      • Poisson.initialize_script_filters()
      • Poisson.preprocessing()
    • Scripter
      • Scripter.__init__()
      • Scripter.add_filters()
      • Scripter.add_params()
      • Scripter.adjust_param()
      • Scripter.combine_dicts()
      • Scripter.create_filter()
      • Scripter.create_param()
      • Scripter.delete_filter()
      • Scripter.delete_param()
      • Scripter.filters
      • Scripter.mls_buffer
      • Scripter.set_filter()
      • Scripter.set_param()
      • Scripter.test_filters()
      • Scripter.to_file()
    • clear_meshlab_port()
    • set_meshlab_port()
  • mesh_tools.meshparty_skeletonize module
    • branches_from_mesh()
    • calculate_skeleton_paths_on_mesh()
    • collapse_soma_skeleton()
    • compute_segments()
    • mesh_teasar()
    • ray_trace_distance()
    • reduce_verts()
    • setup_root()
    • skeleton_obj_to_branches()
    • skeletonize()
    • skeletonize_components()
    • skeletonize_mesh()
    • skeletonize_mesh_largest_component()
    • smooth_graph()
    • width_median_weighted()
  • mesh_tools.skeleton_utils module
    • accuracy_stats_from_true_predicted_skeleton()
    • add_and_smooth_segment_to_branch()
    • align_skeletons_at_connectivity()
    • angle_between_skeleton_vectors_and_ref_vector()
    • bbox()
    • bbox_volume()
    • bounding_box_corners()
    • calcification()
    • calculate_coordinate_distances_cumsum()
    • calculate_skeletal_distance()
    • calculate_skeletal_length()
    • calculate_skeleton_distance()
    • calculate_skeleton_segment_distances()
    • center_skeleton()
    • change_basis_matrix()
    • check_correspondence_branches_have_2_endpoints()
    • check_skeleton_connected_component()
    • check_skeleton_one_component()
    • clean_skeleton()
    • clean_skeleton_with_decompose()
    • clean_skeleton_with_soma_verts()
    • closest_distances_from_skeleton_vertices_to_base_skeleton()
    • closest_skeleton_coordinate()
    • closest_skeleton_coordinates()
    • combine_close_branch_points()
    • compare_endpoints()
    • compare_skeletons_ordered()
    • convert_branch_graph_to_skeleton()
    • convert_graph_to_skeleton()
    • convert_nodes_edges_to_skeleton()
    • convert_skeleton_to_coordinates()
    • convert_skeleton_to_graph()
    • convert_skeleton_to_graph_old()
    • convert_skeleton_to_nodes()
    • convert_skeleton_to_nodes_edges()
    • convert_skeleton_to_nodes_edges_old()
    • convert_skeleton_to_nodes_edges_optimized()
    • convert_skeleton_to_nodes_edges_optimized_old()
    • coordinate_restriction_to_skeleton()
    • coordinates_along_skeleton_offset_from_start()
    • coordinates_from_downstream_dist()
    • create_soma_extending_branches()
    • cut_skeleton_at_coordinate()
    • decompose_skeleton_to_branches()
    • divide_branch()
    • downsample_skeleton()
    • empty_skeleton()
    • endpoint_connectivity()
    • example_cgal_skeletonization_original_params()
    • filter_away_leaf_skeletons()
    • filter_away_small_skeleton_offshoots()
    • find_branch_endpoints()
    • find_branch_skeleton_with_specific_coordinate()
    • find_end_nodes_with_significant_mesh_correspondence()
    • find_skeleton_endpoint_coordinates()
    • flip_skeleton()
    • generate_surface_skeleton()
    • generate_surface_skeleton_slower()
    • get_ordered_branch_nodes_coordinates()
    • gram_schmidt_columns()
    • graph_skeleton_and_mesh()
    • high_degree_coordinates_on_path()
    • high_degree_coordinates_on_skeleton()
    • intersect_skeleton()
    • jitter_skeleton_from_coordinate()
    • kd_tree_from_unique_coordinates()
    • list_len_measure()
    • map_between_branches_lists()
    • map_between_branches_lists_old()
    • matching_endpoint_singular()
    • matching_skeleton_branches_by_endpoints()
    • matching_skeleton_branches_by_vertices()
    • mesh_restriction_to_skeleton()
    • mesh_subtraction_by_skeleton()
    • mesh_subtraction_by_skeleton_old()
    • move_point_to_nearest_branch_end_point_within_threshold()
    • node_names_and_coord_from_G()
    • number_connected_components()
    • number_connected_components_branches()
    • offset_skeletons_aligned_at_shared_endpoint()
    • offset_skeletons_aligned_parent_child_skeletal_angle()
    • old_combine_close_branch_points()
    • order_resize_skeleton()
    • order_skeleton()
    • order_skeletons_connecting_endpoints()
    • parent_child_skeletal_angle()
    • path_ordered_skeleton()
    • percentage_skeleton_match_to_ref_vector()
    • plot_ipv_mesh()
    • plot_ipv_scatter()
    • plot_ipv_skeleton()
    • read_skeleton_edges_coordinates()
    • read_skeleton_verts_edges()
    • recompose_skeleton_from_branches()
    • remove_cycles_from_skeleton()
    • resize_and_center_skeleton()
    • resize_center_and_coordinates_from_skeleton()
    • resize_skeleton_branch()
    • resize_skeleton_with_branching()
    • restrict_skeleton_from_start()
    • restrict_skeleton_from_start_plus_offset()
    • restrict_skeleton_to_distance_from_coordinate()
    • save_skeleton_cgal()
    • setdiff_skeleton()
    • setup_root()
    • shared_coordiantes()
    • shared_endpoint()
    • shortest_path_between_two_sets_of_skeleton_coordiantes()
    • skeletal_distance()
    • skeleton_cgal()
    • skeleton_cgal_original_parameters()
    • skeleton_connected_components()
    • skeleton_coordinate_offset_from_endpoint()
    • skeleton_coordinate_path_from_start()
    • skeleton_endpoint_vector()
    • skeleton_from_h5py()
    • skeleton_graph_nodes_to_group()
    • skeleton_list_connectivity()
    • skeleton_list_connectivity_slow()
    • skeleton_n_components()
    • skeleton_path_between_skeleton_coordinates()
    • skeleton_unique_coordinates()
    • skeleton_vectors()
    • skeletonize_and_clean_connected_branch_CGAL()
    • skeletonize_connected_branch()
    • skeletonize_connected_branch_meshparty()
    • skelton_coordinate_path_to_skeleton()
    • smooth_skeleton_branch()
    • soma_skeleton_stitching()
    • split_skeleton_into_edges()
    • stack_skeletons()
    • stitch_skeleton()
    • subskeleton_from_vertices_idx()
    • subtract_exact_coordinates_from_skeleton()
    • surface_skeleton()
    • vector_away_from_endpoint()
  • mesh_tools.trimesh_utils module
    • area()
    • area_of_vertex_boundary()
    • bbox_intersect_test()
    • bbox_max_x()
    • bbox_max_y()
    • bbox_max_z()
    • bbox_mesh()
    • bbox_mesh_restriction()
    • bbox_min_x()
    • bbox_min_y()
    • bbox_min_z()
    • bbox_side_length_ratios()
    • bbox_volume()
    • bbox_volume_oriented()
    • border_euclidean_length()
    • bounding_box()
    • bounding_box_center()
    • bounding_box_corner_max()
    • bounding_box_corner_min()
    • bounding_box_corners()
    • bounding_box_longest_side()
    • bounding_box_oriented_side_lengths()
    • box_mesh()
    • center_at_origin()
    • center_mesh()
    • center_mesh_at_point()
    • centered_at_origin()
    • check_coordinates_inside_bounding_box()
    • check_meshes_inside_mesh_bbox()
    • check_meshes_inside_multiple_mesh_bbox()
    • check_meshes_outside_mesh_bbox()
    • check_meshes_outside_multiple_mesh_bbox()
    • close_hole_area_max()
    • close_hole_area_top_2_mean()
    • close_hole_area_top_k_extrema()
    • close_hole_areas()
    • close_mesh_holes()
    • close_mesh_holes_at_vertices()
    • closest_connected_component_mesh_to_coordinates()
    • closest_coordinate_to_mesh_faces()
    • closest_distance_between_meshes()
    • closest_face_to_coordinate()
    • closest_face_to_coordinate_distance()
    • closest_face_to_coordinates()
    • closest_face_to_mesh_center_distance()
    • closest_mesh_attribute_to_coordinates_fast()
    • closest_mesh_coordinate_to_other_mesh()
    • closest_mesh_distance_to_coordinates_fast()
    • closest_mesh_to_coordinate()
    • closest_mesh_to_coordinates()
    • closest_mesh_to_mesh()
    • closest_mesh_vertex_to_other_mesh()
    • closest_n_attributes_to_coordinate()
    • closest_segmentation_to_coordinate()
    • closest_split_to_coordinate()
    • combine_meshes()
    • compare_meshes_by_face_midpoints()
    • compare_meshes_by_face_midpoints_list()
    • components_to_submeshes()
    • connected_component_meshes()
    • connected_components_from_face_idx()
    • connected_components_from_mesh()
    • connected_nondegenerate_mesh()
    • convert_meshes_to_face_idxes()
    • convert_o3d_to_trimesh()
    • convert_trimesh_to_o3d()
    • coordinate_on_mesh_mesh_border()
    • coordinates_to_bounding_box()
    • coordinates_to_enclosing_sphere()
    • coordinates_to_enclosing_sphere_center_radius()
    • coordinates_to_enclosing_sphere_volume()
    • decimate()
    • default_mesh_stats_to_run()
    • divide_mesh_into_connected_components()
    • empty_mesh()
    • expand_border_faces()
    • export_mesh()
    • face_idx_map_from_face_idx_list()
    • face_midpoints_x_z()
    • face_neighbors_by_vertices()
    • face_neighbors_by_vertices_seperate()
    • faces_closer_than_distance_of_coordinates()
    • faces_defined_by_vertices_idx_list_to_mesh()
    • faces_farther_than_distance_of_coordinates()
    • farthest_coordinate_to_faces()
    • farthest_face_to_coordinate()
    • farthest_face_to_coordinate_distance()
    • farthest_face_to_mesh_center_distance()
    • fill_holes()
    • fill_holes_trimesh()
    • fill_mesh_holes()
    • fill_mesh_holes_with_fan()
    • fill_single_triangle_holes()
    • filter_away_border_touching_submeshes_by_group()
    • filter_away_connected_comp_in_face_idx_with_minimum_vertex_distance_to_coordinates()
    • filter_away_inside_meshes()
    • filter_meshes_by_bounding_box_longest_side()
    • filter_meshes_by_containing_coordinates()
    • filter_meshes_by_size()
    • filter_meshes_by_size_min_max()
    • filter_vertices_by_mesh()
    • find_border_face_groups()
    • find_border_faces()
    • find_border_vertex_groups()
    • find_border_vertices()
    • find_closest_coordinate_to_mesh_faces()
    • find_closest_face_to_coordinates()
    • find_degenerate_faces()
    • find_large_dense_submesh()
    • find_nondegenerate_faces()
    • get_non_manifold_edges()
    • get_non_manifold_vertices()
    • interpercentile_range_face_midpoints()
    • interpercentile_range_face_midpoints_volume()
    • interpercentile_range_face_midpoints_x()
    • interpercentile_range_face_midpoints_y()
    • interpercentile_range_face_midpoints_z()
    • ipr_first_second_largest_eigenvector_xz_diff()
    • ipr_largest_eigenvector_xy()
    • ipr_largest_eigenvector_xz()
    • ipr_second_largest_eigenvector_xz()
    • is_manifold()
    • is_mesh()
    • is_watertight()
    • kdtree_length()
    • largest_border_to_coordinate()
    • largest_conn_comp()
    • largest_hole_length()
    • load_mesh_no_processing()
    • load_mesh_no_processing_h5()
    • max_distance_betwee_mesh_vertices()
    • mesh_bbox_contains_skeleton()
    • mesh_center_vertex_average()
    • mesh_center_weighted_face_midpoints()
    • mesh_centered_at_origin()
    • mesh_face_graph_by_vertex()
    • mesh_from_vertices_faces()
    • mesh_interior()
    • mesh_kdtree_face()
    • mesh_kdtree_vertices()
    • mesh_list_connectivity()
    • mesh_list_distance_connectivity()
    • mesh_overlap_with_restriction_mesh()
    • mesh_pieces_connectivity()
    • mesh_segmentation()
    • mesh_segmentation_from_skeleton()
    • mesh_segmentation_largest_conn_comp()
    • mesh_size()
    • mesh_stats()
    • mesh_to_kdtree()
    • mesh_vertex_graph()
    • mesh_volume()
    • mesh_volume_convex_hull()
    • mesh_volume_o3d()
    • mesh_volume_ratio()
    • mesh_with_ends_cutoff()
    • meshes_distance_matrix()
    • meshes_within_close_proximity()
    • min_cut_to_partition_mesh_vertices()
    • n_faces()
    • n_vertices_inside_mesh_bbox()
    • n_vertices_outside_mesh_bbox()
    • original_mesh_faces_map()
    • original_mesh_vertices_map()
    • overlapping_attribute()
    • overlapping_faces()
    • overlapping_vertices()
    • overlapping_vertices_from_face_lists()
    • percentage_vertices_inside()
    • plot_segmentation()
    • poisson_surface_reconstruction()
    • pymeshfix_clean()
    • query_meshes_from_restrictions()
    • query_meshes_from_stats()
    • radius_sphere_from_volume()
    • ratio_closest_face_to_mesh_center_distance_to_width()
    • ratio_farthest_face_to_mesh_center_distance_to_width()
    • ratio_ipr_eigenvector_xz_diff_to_width()
    • ratio_mesh_stat_to_width()
    • ray_trace_distance()
    • ray_trace_distance_by_mesh_center_dist()
    • remove_degenerate_faces()
    • remove_mesh_interior()
    • restrict_mesh()
    • restrict_mesh_list_by_mesh()
    • restrict_meshes_from_stats()
    • rotate_mesh_from_matrix()
    • scatter_mesh_with_radius()
    • shared_edges_between_faces_on_mesh()
    • skeletal_length_from_mesh()
    • skeleton_and_mesh_segmentation()
    • skeleton_non_branching_from_mesh()
    • skeleton_to_mesh_correspondence()
    • sort_meshes_largest_to_smallest()
    • sphere_mesh()
    • split()
    • split_by_vertices()
    • split_mesh_by_closest_skeleton()
    • split_mesh_into_face_groups()
    • split_significant_pieces()
    • split_significant_pieces_old()
    • split_vertex_list_into_connected_components()
    • split_vertex_list_into_connected_components_old()
    • stats_df()
    • stitch()
    • stitch_mesh_at_vertices()
    • stitch_mesh_holes()
    • submesh()
    • subtract_mesh()
    • surface_area()
    • surface_area_to_volume()
    • test_inside_meshes()
    • translate_mesh()
    • turn_off_logging()
    • two_mesh_list_connectivity()
    • valid_coordiantes_mapped_to_mesh()
    • vertex_components()
    • vertex_indices_subgraph()
    • vertices_coordinates_to_faces()
    • vertices_coordinates_to_faces_old()
    • vertices_coordinates_to_vertex_index()
    • vertices_mask_inside_mesh_bbox()
    • vertices_mask_inside_meshes_bbox()
    • vertices_to_faces()
    • waterfilling_face_idx()
    • width_of_submesh()
    • width_ray()
    • width_ray_trace_median()
    • width_ray_trace_perc()
    • width_ray_trace_perc_of_submesh()
    • widths_of_submeshes()
    • write_h5_file()
    • write_neuron_off()
  • Module contents