Index

A

add_bspline_filling() (gmsh_mesh_builder.Mesher method) add_curve_loop() (quad_refinement.QuadRefinement method) add_interslice_segments() (gmsh_mesh_builder.Mesher method) add_intersurface_planes() (gmsh_mesh_builder.Mesher method)

add_slice_surfaces() (gmsh_mesh_builder.Mesher method) add_surface_loop() (quad_refinement.QuadRefinement method) add_volume() (gmsh_mesh_builder.Mesher method) analyse_mesh_quality() (gmsh_mesh_builder.Mesher method)

C

calculate_outer_offset() (spline_volume.OCC_volume method) ccw_angle() (cortical_sanity.CorticalSanityCheck method) center_of_mass() (cortical_sanity.CorticalSanityCheck method) (quad_refinement.QuadRefinement method) check_closed_surface_loop() (quad_refinement.QuadRefinement method) check_inner_offset() (spline_volume.OCC_volume method) check_min_thickness() (cortical_sanity.CorticalSanityCheck method) check_orient() (spline_volume.OCC_volume method) classify_and_store_contours() (spline_volume.OCC_volume method) close_outer_loop() (quad_refinement.QuadRefinement method) common() (quad_refinement.QuadRefinement method) convertRadiansToDegrees() (cortical_sanity.CorticalSanityCheck method) correct_internal_point() (cortical_sanity.CorticalSanityCheck method)

correct_intersection() (cortical_sanity.CorticalSanityCheck method) cortical_sanity module cortical_sanity_check() (cortical_sanity.CorticalSanityCheck method) CorticalSanityCheck (class in cortical_sanity) create_centre_splines() (gmsh_mesh_builder.Mesher method) create_connecting_surfaces() (quad_refinement.QuadRefinement method) create_initial_points() (in module quad_refinement) create_intersurface_connection() (quad_refinement.QuadRefinement method) create_line_dict() (quad_refinement.QuadRefinement method) create_square_grid() (quad_refinement.QuadRefinement method) create_subvertices() (quad_refinement.QuadRefinement method) create_surf_dict() (quad_refinement.QuadRefinement method)

D

draw_arrow() (cortical_sanity.CorticalSanityCheck method)

draw_contours() (spline_volume.OCC_volume method)

E

err() (spline_volume.OCC_volume method) evaluate_bspline() (spline_volume.OCC_volume method)

exec_quad_refinement() (quad_refinement.QuadRefinement method) exec_thresholding() (spline_volume.OCC_volume method)

F

flatten() (quad_refinement.QuadRefinement method)

G

get_adjacent_points() (quad_refinement.QuadRefinement method) get_affine_transformation_matrix() (quad_refinement.QuadRefinement method) get_barycenters() (gmsh_mesh_builder.Mesher method) get_binary_contour() (spline_volume.OCC_volume method) get_centroids_dict() (gmsh_mesh_builder.Mesher method) get_common_lines() (quad_refinement.QuadRefinement method) get_draw_contour() (spline_volume.OCC_volume method) get_elm_volume() (gmsh_mesh_builder.Mesher method) get_line_sets() (spline_volume.OCC_volume method) get_normals() (cortical_sanity.CorticalSanityCheck method) get_offset_points() (gmsh_mesh_builder.TrabecularVolume method) get_radius_longest_edge() (gmsh_mesh_builder.Mesher method) get_sort_coords() (gmsh_mesh_builder.Mesher method) get_trabecular_cortical_volume_mesh() (gmsh_mesh_builder.Mesher method) get_trabecular_position() (gmsh_mesh_builder.TrabecularVolume method) get_trabecular_vol() (gmsh_mesh_builder.TrabecularVolume method) get_vertices_coords() (gmsh_mesh_builder.TrabecularVolume method) (quad_refinement.QuadRefinement method) get_vertices_minmax() (quad_refinement.QuadRefinement method) gmsh_add_custom_lines() (quad_refinement.QuadRefinement method)

gmsh_add_line() (quad_refinement.QuadRefinement method) gmsh_add_outer_connectivity() (quad_refinement.QuadRefinement method) gmsh_add_plane_surface() (quad_refinement.QuadRefinement method) gmsh_add_points() (gmsh_mesh_builder.Mesher method) (quad_refinement.QuadRefinement method) gmsh_add_surface() (quad_refinement.QuadRefinement method) gmsh_add_surfaces() (quad_refinement.QuadRefinement method) gmsh_add_surfs() (quad_refinement.QuadRefinement method) gmsh_add_volume() (quad_refinement.QuadRefinement method) gmsh_geometry_formulation() (gmsh_mesh_builder.Mesher method) gmsh_get_bnds() (gmsh_mesh_builder.Mesher method) gmsh_get_elms() (gmsh_mesh_builder.Mesher method) gmsh_get_nodes() (gmsh_mesh_builder.Mesher method) gmsh_get_reference_point_coord() (gmsh_mesh_builder.Mesher method) gmsh_get_unique_surfaces() (quad_refinement.QuadRefinement method) gmsh_insert_bspline() (gmsh_mesh_builder.Mesher method) gmsh_make_transfinite() (quad_refinement.QuadRefinement method) gmsh_mesh_builder module gmsh_skin_points() (quad_refinement.QuadRefinement method) guess() (spline_volume.OCC_volume method)

H

HexMesh (class in spline_mesher)

hyp_min_thickness() (cortical_sanity.CorticalSanityCheck method)

I

input_sanity_check() (spline_volume.OCC_volume method) insert_bspline() (gmsh_mesh_builder.Mesher method) insert_closest_point() (gmsh_mesh_builder.Mesher method) insert_ellipse_arcs() (gmsh_mesh_builder.Mesher method) insert_intersection_line() (gmsh_mesh_builder.Mesher method) insert_lines() (gmsh_mesh_builder.Mesher method)

insert_points() (gmsh_mesh_builder.Mesher method) insert_tensor_of_inertia() (gmsh_mesh_builder.Mesher method) interpolate_vertical_lines_3d() (spline_volume.OCC_volume method) intersection_point() (gmsh_mesh_builder.Mesher method) is_angle_bigger_bool() (cortical_sanity.CorticalSanityCheck method) is_internal_inside_external() (cortical_sanity.CorticalSanityCheck method) is_internal_radius_bigger_than_external() (cortical_sanity.CorticalSanityCheck method)

K

KDT_nn() (cortical_sanity.CorticalSanityCheck method)

L

lineseg_dists() (cortical_sanity.CorticalSanityCheck method)

M

mesh_generate() (gmsh_mesh_builder.Mesher method) Mesher (class in gmsh_mesh_builder) mesher() (spline_mesher.HexMesh method) meshing_transfinite() (gmsh_mesh_builder.Mesher method) min_thickness_nearest_pairs() (cortical_sanity.CorticalSanityCheck method)

module cortical_sanity gmsh_mesh_builder quad_refinement spline_mesher spline_volume

N

nearest_pairs_arrs() (cortical_sanity.CorticalSanityCheck method)

nearest_point() (cortical_sanity.CorticalSanityCheck method) nodes2coords() (gmsh_mesh_builder.Mesher method)

O

OCC_volume (class in spline_volume)

offset_surface() (cortical_sanity.CorticalSanityCheck method) output_sanity_check() (spline_volume.OCC_volume method)

P

pad_and_plot() (spline_volume.OCC_volume method) pad_image() (spline_volume.OCC_volume method) partition_lines() (gmsh_mesh_builder.Mesher method) plot_contours() (cortical_sanity.CorticalSanityCheck method) plot_corrected_contours() (cortical_sanity.CorticalSanityCheck method) plot_mhd_slice() (spline_volume.OCC_volume method) plot_slice() (spline_volume.OCC_volume method) plot_slices_with_slider() (spline_volume.OCC_volume method)

plot_vertices() (quad_refinement.QuadRefinement method) plotly_add_traces() (spline_volume.OCC_volume method) plotly_makefig() (spline_volume.OCC_volume method) polygon_tensor_of_inertia() (gmsh_mesh_builder.Mesher method) principal_axes_length() (gmsh_mesh_builder.TrabecularVolume method) process_slice() (spline_volume.OCC_volume method) project_point_on_line() (cortical_sanity.CorticalSanityCheck method) push_contour() (cortical_sanity.CorticalSanityCheck method)

Q

quad_refinement module

quad_refinement() (quad_refinement.QuadRefinement method) QuadRefinement (class in quad_refinement) query_closest_idx() (gmsh_mesh_builder.Mesher method)

R

resample_contour() (cortical_sanity.CorticalSanityCheck method)

reset_numpy_index() (cortical_sanity.CorticalSanityCheck method) roll_index() (cortical_sanity.CorticalSanityCheck method)

S

set_length_factor() (gmsh_mesh_builder.TrabecularVolume method) set_transformation_matrix() (quad_refinement.QuadRefinement method) shapely_line_polygon_intersection() (gmsh_mesh_builder.Mesher method) shift_point() (gmsh_mesh_builder.Mesher method) sort_bspline_cw() (gmsh_mesh_builder.Mesher method) sort_by_indexes() (gmsh_mesh_builder.Mesher method) sort_ccw() (gmsh_mesh_builder.Mesher method) sort_intersection_points() (gmsh_mesh_builder.Mesher method) sort_mahalanobis() (spline_volume.OCC_volume method)

sort_surface() (spline_volume.OCC_volume method) sort_trab_coords() (gmsh_mesh_builder.TrabecularVolume method) sort_xy() (spline_volume.OCC_volume method) spline_mesher module spline_neumann() (spline_volume.OCC_volume method) spline_volume module split_dict_by_array_len() (gmsh_mesh_builder.Mesher method)

T

trabecular_cortical_connection() (gmsh_mesh_builder.Mesher method) trabecular_planes_inertia() (gmsh_mesh_builder.Mesher method)

trabecular_slices() (gmsh_mesh_builder.Mesher method) TrabecularVolume (class in gmsh_mesh_builder)

U

unit_vector() (cortical_sanity.CorticalSanityCheck method)

V

vertices_grid_cleanup() (quad_refinement.QuadRefinement method)

volume_splines() (spline_volume.OCC_volume method) volume_splines_optimized() (spline_volume.OCC_volume method)