Index _ | A | B | C | D | E | F | G | I | J | L | M | N | O | P | R | S | T | V | X _ __init__() (mascaf.basis_optimizer.BasisOptimizer method) (mascaf.basis_optimizer.BasisOptimizerOptions method) (mascaf.cable_fitting.CableFitter method) (mascaf.cable_fitting.FitOptions method) (mascaf.cgal.CGALBuilder method) (mascaf.cgal.CGALCommandResult method) (mascaf.cgal.CGALConfig method) (mascaf.cgal.CGALOperator method) (mascaf.mesh.MeshManager method) (mascaf.morphology_graph.Junction method) (mascaf.morphology_graph.MorphologyGraph method) (mascaf.skeleton.SkeletonGraph method) (mascaf.validation.Validation method) A add_junction() (mascaf.morphology_graph.MorphologyGraph method) analyze_mesh() (mascaf.mesh.MeshManager method) B basis_optimizer_options (mascaf.cable_fitting.FitOptions attribute) BasisOptimizer (class in mascaf.basis_optimizer) BasisOptimizerOptions (class in mascaf.basis_optimizer) bounding_box_diagonal() (mascaf.mesh.MeshManager method) bounds() (mascaf.graph3d.Graph3D method) build_command() (mascaf.cgal.CGALBuilder method) build_configs (mascaf.cgal.CGALConfig attribute), [1] build_dir (mascaf.cgal.CGALConfig attribute), [1] build_graph() (mascaf.skeleton.SkeletonGraph method) C CableFitter (class in mascaf.cable_fitting) candidate_build_dirs() (mascaf.cgal.CGALBuilder method) candidate_executable_dirs() (mascaf.cgal.CGALBuilder method) CGALBuilder (class in mascaf.cgal) CGALBuildError CGALCommandResult (class in mascaf.cgal) CGALConfig (class in mascaf.cgal) CGALError CGALExecutableNotFoundError CGALMeshProcessor (in module mascaf.cgal) CGALOperator (class in mascaf.cgal) cmake_executable (mascaf.cgal.CGALConfig attribute), [1] command (mascaf.cgal.CGALCommandResult attribute), [1] compare_surface_areas() (mascaf.validation.Validation method) compare_volumes() (mascaf.validation.Validation method) compute_branch_lengths() (mascaf.skeleton.SkeletonGraph method) compute_surface_area() (mascaf.morphology_graph.MorphologyGraph method) compute_volume() (mascaf.morphology_graph.MorphologyGraph method) configure_command() (mascaf.cgal.CGALBuilder method) convergence_threshold (mascaf.basis_optimizer.BasisOptimizerOptions attribute) copy() (mascaf.mesh.MeshManager method) (mascaf.morphology_graph.MorphologyGraph method) (mascaf.skeleton.SkeletonGraph method) cpp_dir (mascaf.cgal.CGALConfig attribute), [1] D default_build_dir() (mascaf.cgal.CGALConfig method) detect_branch_points() (mascaf.skeleton.SkeletonGraph method) do_forcing (mascaf.basis_optimizer.BasisOptimizerOptions attribute) do_pruning (mascaf.basis_optimizer.BasisOptimizerOptions attribute) do_snapping (mascaf.basis_optimizer.BasisOptimizerOptions attribute) E example_mesh() (in module mascaf.mesh) executable_dir (mascaf.cgal.CGALConfig attribute), [1] executable_filename() (mascaf.cgal.CGALBuilder method) executable_suffix (mascaf.cgal.CGALConfig attribute), [1] F fallback_distance (mascaf.basis_optimizer.BasisOptimizerOptions attribute) fit() (mascaf.cable_fitting.CableFitter method) FitOptions (class in mascaf.cable_fitting) from_overrides() (mascaf.cgal.CGALConfig class method) from_polylines() (mascaf.skeleton.SkeletonGraph class method) from_swc_file() (mascaf.morphology_graph.MorphologyGraph class method) from_txt() (mascaf.skeleton.SkeletonGraph class method) full_validation() (mascaf.validation.Validation method) G get_all_positions() (mascaf.graph3d.Graph3D method) get_branch_nodes() (mascaf.graph3d.Graph3D method) get_branch_point_indices() (mascaf.skeleton.SkeletonGraph method) get_continuation_nodes() (mascaf.graph3d.Graph3D method) get_node_position() (mascaf.graph3d.Graph3D method) get_optimization_stats() (mascaf.basis_optimizer.BasisOptimizer method) get_outside_nodes() (mascaf.basis_optimizer.BasisOptimizer method) get_statistics() (mascaf.skeleton.SkeletonGraph method) get_terminal_nodes() (mascaf.graph3d.Graph3D method) get_total_length() (mascaf.graph3d.Graph3D method) (mascaf.skeleton.SkeletonGraph method) get_true_endpoint_indices() (mascaf.skeleton.SkeletonGraph method) Graph3D (class in mascaf.graph3d) I id (mascaf.morphology_graph.Junction attribute) input_path (mascaf.cgal.CGALCommandResult attribute), [1] is_branch_node() (mascaf.graph3d.Graph3D method) is_continuation_node() (mascaf.graph3d.Graph3D method) is_terminal_node() (mascaf.graph3d.Graph3D method) J Junction (class in mascaf.morphology_graph) L load_mesh() (mascaf.mesh.MeshManager method) M mascaf.basis_optimizer module mascaf.cable_fitting module mascaf.cgal module mascaf.graph3d module mascaf.mesh module mascaf.morphology_graph module mascaf.skeleton module mascaf.validation module mascaf.visualization module max_edge_length (mascaf.cable_fitting.FitOptions attribute) max_iterations (mascaf.basis_optimizer.BasisOptimizerOptions attribute) mesh (mascaf.validation.Validation attribute) mesh_manager (mascaf.validation.Validation attribute) MeshManager (class in mascaf.mesh) midpoint() (mascaf.graph3d.Graph3D method) module mascaf.basis_optimizer mascaf.cable_fitting mascaf.cgal mascaf.graph3d mascaf.mesh mascaf.morphology_graph mascaf.skeleton mascaf.validation mascaf.visualization morphology (mascaf.validation.Validation attribute) MorphologyGraph (class in mascaf.morphology_graph) multi_tangent_reduction (mascaf.cable_fitting.FitOptions attribute) N n_rays (mascaf.basis_optimizer.BasisOptimizerOptions attribute) O operation (mascaf.cgal.CGALCommandResult attribute), [1] optimize() (mascaf.basis_optimizer.BasisOptimizer method) output_path (mascaf.cgal.CGALCommandResult attribute), [1] P plot_surface_mesh_grid() (in module mascaf.visualization) position_attr (mascaf.graph3d.Graph3D attribute) (mascaf.morphology_graph.MorphologyGraph attribute) (mascaf.skeleton.SkeletonGraph attribute) preserve_branch_nodes (mascaf.basis_optimizer.BasisOptimizerOptions attribute) preserve_terminal_nodes (mascaf.basis_optimizer.BasisOptimizerOptions attribute) print_attributes() (mascaf.morphology_graph.MorphologyGraph method) print_mesh_analysis() (mascaf.mesh.MeshManager method) prune_short_branches() (mascaf.skeleton.SkeletonGraph method) prune_short_branches_inplace() (mascaf.skeleton.SkeletonGraph method) pruning_iterative (mascaf.basis_optimizer.BasisOptimizerOptions attribute) pruning_min_length (mascaf.basis_optimizer.BasisOptimizerOptions attribute) pruning_min_length_fraction (mascaf.basis_optimizer.BasisOptimizerOptions attribute) R radius (mascaf.morphology_graph.Junction attribute) radius_strategy (mascaf.cable_fitting.FitOptions attribute) repair() (mascaf.cgal.CGALOperator method) repair_mesh() (mascaf.mesh.MeshManager method) resample() (mascaf.skeleton.SkeletonGraph method) resolve_executable() (mascaf.cgal.CGALBuilder method) returncode (mascaf.cgal.CGALCommandResult attribute), [1] run_build() (mascaf.cgal.CGALBuilder method) run_configure() (mascaf.cgal.CGALBuilder method) S save() (mascaf.mesh.MeshManager method) save_surface_mesh_grid_svg() (in module mascaf.visualization) save_surface_meshes_svg() (in module mascaf.visualization) scale_radii_to_match_mesh() (mascaf.morphology_graph.MorphologyGraph method) section_probe_eps (mascaf.cable_fitting.FitOptions attribute) section_probe_tries (mascaf.cable_fitting.FitOptions attribute) set_all_positions() (mascaf.graph3d.Graph3D method) set_node_position() (mascaf.graph3d.Graph3D method) simplify() (mascaf.cgal.CGALOperator method) skeleton (mascaf.validation.Validation attribute) SkeletonGraph (class in mascaf.skeleton) skeletonize() (mascaf.cgal.CGALOperator method) smoothing_weight (mascaf.basis_optimizer.BasisOptimizerOptions attribute) snap_distance_multiplier (mascaf.basis_optimizer.BasisOptimizerOptions attribute) snap_to_mesh_surface() (mascaf.skeleton.SkeletonGraph method) stderr (mascaf.cgal.CGALCommandResult attribute), [1] stdout (mascaf.cgal.CGALCommandResult attribute), [1] step_size (mascaf.basis_optimizer.BasisOptimizerOptions attribute) suggest_skeletonization_parameters() (mascaf.cgal.CGALOperator method) swc_path (mascaf.validation.Validation attribute) T to_point_set() (mascaf.skeleton.SkeletonGraph method) to_polylines() (mascaf.skeleton.SkeletonGraph method) to_swc_file() (mascaf.morphology_graph.MorphologyGraph method) to_swc_model() (mascaf.morphology_graph.MorphologyGraph method) to_trimesh() (mascaf.mesh.MeshManager method) to_txt() (mascaf.skeleton.SkeletonGraph method) V Validation (class in mascaf.validation) vcpkg_toolchain_file (mascaf.cgal.CGALConfig attribute), [1] verbose (mascaf.basis_optimizer.BasisOptimizerOptions attribute) visualize_mesh_3d() (mascaf.mesh.MeshManager method) visualize_mesh_slice_interactive() (mascaf.mesh.MeshManager method) X xyz (mascaf.morphology_graph.Junction attribute)