Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Z _ __str__() (topostats.Colormap method) (topostats.theme.Colormap method) __version__ (in module topostats) _angle_between() (in module feret) _binary_final_thin_check_a() (topostats.tracing.skeletonize.topostatsSkeletonize method) _binary_final_thin_check_b() (topostats.tracing.skeletonize.topostatsSkeletonize method) _binary_thin_check_a() (topostats.tracing.skeletonize.topostatsSkeletonize method) _binary_thin_check_b_returncount() (topostats.tracing.skeletonize.topostatsSkeletonize method) _binary_thin_check_c() (topostats.tracing.skeletonize.topostatsSkeletonize method) _binary_thin_check_csharp() (topostats.tracing.skeletonize.topostatsSkeletonize method) _binary_thin_check_d() (topostats.tracing.skeletonize.topostatsSkeletonize method) _binary_thin_check_dsharp() (topostats.tracing.skeletonize.topostatsSkeletonize method) _calculate_centroid() (topostats.grainstats.GrainStats static method) _calculate_displacement() (topostats.grainstats.GrainStats static method) _calculate_local_curvature() (topostats.tracing.dnacurvature.Curvature method) _calculate_radius() (topostats.grainstats.GrainStats static method) _check_image_size_and_add_to_dict() (topostats.io.LoadScans method) _delete_pixel_subit1() (topostats.tracing.skeletonize.topostatsSkeletonize method) _delete_pixel_subit2() (topostats.tracing.skeletonize.topostatsSkeletonize method) _do_skeletonising_iteration() (topostats.tracing.skeletonize.topostatsSkeletonize method) _find_branch_ends() (topostats.tracing.pruning.topostatsPrune static method) _get_abs_thresh_idx() (topostats.tracing.pruning.heightPruning static method) _get_branch_medians() (topostats.tracing.pruning.heightPruning method) _get_branch_middles() (topostats.tracing.pruning.heightPruning method) _get_branch_mins() (topostats.tracing.pruning.heightPruning method) _get_iqr_thresh_idx() (topostats.tracing.pruning.heightPruning static method) _get_mask() (in module topostats.utils) _get_mean_abs_thresh_idx() (topostats.tracing.pruning.heightPruning static method) _get_skeletonize() (topostats.tracing.skeletonize.getSkeleton method) _get_threshold() (in module topostats.thresholds) _log_setup() (in module topostats.run_modules) _mark_if_negative_scar() (in module topostats.scars) _mark_if_positive_scar() (in module topostats.scars) _mark_scars() (in module topostats.scars) _min_feret_coord() (in module feret) _outfile() (topostats.plotting.TopoSum method) _pad_array() (in module topostats.plotting) _parse_configuration() (in module topostats.run_modules) _prune_by_length() (topostats.tracing.pruning.topostatsPrune method) _prune_method() (in module topostats.tracing.pruning) _prune_topostats() (in module topostats.tracing.pruning) _remove_marked_scars() (in module topostats.scars) _remove_re_entering_branches() (topostats.tracing.nodestats.nodeStats static method) _remove_short_scars() (in module topostats.scars) _set_label() (topostats.plotting.TopoSum method) _set_logging() (in module topostats.run_modules) _setup_figure() (topostats.plotting.TopoSum method) _skeletonize_lee() (topostats.tracing.skeletonize.getSkeleton static method) _skeletonize_medial_axis() (topostats.tracing.skeletonize.getSkeleton static method) _skeletonize_thin() (topostats.tracing.skeletonize.getSkeleton static method) _skeletonize_topostats() (topostats.tracing.skeletonize.getSkeleton static method) _skeletonize_zhang() (topostats.tracing.skeletonize.getSkeleton static method) _split_skeleton() (topostats.tracing.pruning.heightPruning static method) _spread_scars() (in module topostats.scars) _threshold_mean() (in module topostats.thresholds) _threshold_minimum() (in module topostats.thresholds) _threshold_otsu() (in module topostats.thresholds) _threshold_triangle() (in module topostats.thresholds) _threshold_yen() (in module topostats.thresholds) A above_below_value_idx() (topostats.tracing.nodestats.nodeStats static method) absolute_area_threshold (topostats.grains.Grains attribute) add_bounding_boxes_to_plot() (in module topostats.plottingfuncs) add_branches_to_labelled_image() (topostats.tracing.nodestats.nodeStats static method) add_pixel_to_nm_to_plotting_config() (in module topostats.plottingfuncs) add_to_dict() (topostats.io.LoadScans method) all_connected_nodes (topostats.tracing.nodestats.nodeStats attribute) all_pairs() (in module feret) all_visuals_img (topostats.tracing.nodestats.nodeStats attribute) alpha (topostats.plotting.TopoSum attribute) analyse_node_branches() (topostats.tracing.nodestats.nodeStats static method) analyse_nodes() (topostats.tracing.nodestats.nodeStats method) angle_diff_signed() (in module curvature) angles (topostats.tracing.nodestats.MatchedBranch attribute) area_thresholding() (topostats.grains.Grains method) assemble_grain_mask_tensor_from_crops() (topostats.grains.Grains static method) average_background() (topostats.filters.Filters method) average_crossing_confs() (topostats.tracing.nodestats.nodeStats static method) average_height_trace() (topostats.tracing.nodestats.nodeStats static method) average_uniques() (topostats.tracing.nodestats.nodeStats static method) axes (topostats.plottingfuncs.Images attribute) B base_dir (topostats.plotting.TopoSum attribute) base_output_dir (topostats.grainstats.GrainStats attribute) best_matches() (topostats.tracing.nodestats.nodeStats static method) binary_line() (topostats.tracing.nodestats.nodeStats static method) binary_thin_check_diag() (topostats.tracing.skeletonize.topostatsSkeletonize method) bins (topostats.plotting.TopoSum attribute) blue() (topostats.Colormap static method) (topostats.theme.Colormap static method) blue_purple_green() (topostats.Colormap static method) (topostats.theme.Colormap static method) bound_padded_coordinates_to_image() (in module topostats.utils) bounding_box_cartesian_points_float() (in module geometry) bounding_box_cartesian_points_integer() (in module geometry) bounding_boxes (topostats.grains.Grains attribute) branch_pairing_length (topostats.tracing.nodestats.nodeStats attribute) branch_stats (topostats.tracing.nodestats.NodeDict attribute) C calc_angles() (topostats.tracing.nodestats.nodeStats static method) calc_diff() (topostats.filters.Filters static method) calc_gradient() (topostats.filters.Filters method) calc_minimum_grain_size() (topostats.grains.Grains method) calculate_aspect_ratio() (topostats.grainstats.GrainStats method) calculate_curvature_stats_image() (in module curvature) calculate_derivatives() (topostats.tracing.dnacurvature.Curvature method) calculate_dna_width() (topostats.tracing.disordered_tracing.disorderedTrace static method) calculate_edges() (topostats.grainstats.GrainStats static method) calculate_fwhm() (topostats.tracing.nodestats.nodeStats static method) calculate_points() (topostats.grainstats.GrainStats static method) calculate_radius_stats() (topostats.grainstats.GrainStats method) calculate_region_connection_regions() (topostats.grains.Grains static method) calculate_shortest_branch_distances() (in module geometry) calculate_squared_distance() (topostats.grainstats.GrainStats method) calculate_stats() (topostats.grainstats.GrainStats method) channel (topostats.io.LoadScans attribute) channel_data (topostats.io.LoadScans attribute) check_node_errorless() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) check_run_steps() (in module topostats.processing) check_skeleton_one_object() (topostats.tracing.pruning.heightPruning static method) check_vectors_candidate_points() (topostats.tracing.tracingfuncs.genTracingFuncs static method) circular (topostats.tracing.dnacurvature.Curvature attribute) circularTrace() (topostats.tracing.tracingfuncs.reorderTrace static method) classes_to_merge (topostats.grains.Grains attribute) cmap (topostats.Colormap attribute) (topostats.plottingfuncs.Images attribute) (topostats.theme.Colormap attribute) colorbar (topostats.plottingfuncs.Images attribute) Colormap (class in topostats) (class in topostats.theme) colour_regions() (topostats.grains.Grains method) COLUMN_SETS (in module topostats.utils) compile_images() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) compile_metrics() (topostats.tracing.nodestats.nodeStats method) compile_skan_stats() (in module topostats.tracing.disordered_tracing) compile_trace() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) completion_message() (in module topostats.processing) confidence (topostats.tracing.nodestats.NodeDict attribute) CONFIG_DOCUMENTATION_REFERENCE (in module topostats.io) connect_best_matches() (in module geometry) connect_close_nodes() (topostats.tracing.nodestats.nodeStats method) connect_extended_nodes_nearest() (topostats.tracing.nodestats.nodeStats method) connected_nodes (topostats.tracing.nodestats.nodeStats attribute) conv_skelly (topostats.tracing.nodestats.nodeStats attribute) convert_basename_to_relative_paths() (in module topostats.io) convert_classes_to_nearby_classes() (topostats.grains.Grains static method) convert_classes_when_too_big_or_small() (topostats.grains.Grains static method) convert_path() (in module topostats.utils) convex_hull() (topostats.grainstats.GrainStats method) convolve_skeleton() (in module topostats.utils) (topostats.tracing.pruning.heightPruning method) coord_dist() (in module topostats.tracing.tracingfuncs) coord_dist_rad() (topostats.tracing.nodestats.nodeStats static method) coords_2_img() (in module topostats.utils) core_set (topostats.plottingfuncs.Images attribute) count_and_get_neighbours() (topostats.tracing.tracingfuncs.genTracingFuncs static method) counter (topostats.tracing.skeletonize.topostatsSkeletonize attribute) create_empty_dataframe() (in module topostats.utils) create_parser() (in module topostats.entry_point) create_weighted_graph() (topostats.tracing.nodestats.nodeStats static method) crop_array() (in module topostats.tracing.disordered_tracing) cropped_size (topostats.grainstats.GrainStats attribute) cross_confidence() (topostats.tracing.nodestats.nodeStats static method) curvature module Curvature (class in topostats.tracing.dnacurvature) cut (topostats.plotting.TopoSum attribute) D data (topostats.grainstats.GrainStats attribute) (topostats.plottingfuncs.Images attribute) DEFAULT_CONFIG_SCHEMA (in module topostats.validation) df (topostats.plotting.TopoSum attribute) dice_loss() (in module topostats.unet_masking) dict_almost_equal() (in module topostats.io) dict_to_hdf5() (in module topostats.io) dict_to_json() (in module topostats.io) dilate_binary_image() (in module topostats.plottingfuncs) direction (topostats.grains.Grains attribute) (topostats.grainstats.GrainStats attribute) directions (topostats.grains.Grains attribute) discrete_angle_difference_per_nm_circular() (in module curvature) discrete_angle_difference_per_nm_linear() (in module curvature) disordered_trace (topostats.tracing.disordered_tracing.disorderedTrace attribute) disordered_trace_grain() (in module topostats.tracing.disordered_tracing) disordered_tracing() (in module topostats.run_modules) disorderedTrace (class in topostats.tracing.disordered_tracing) distances (topostats.tracing.nodestats.MatchedBranch attribute) do_points_in_arrays_touch() (in module geometry) do_skeletonising() (topostats.tracing.skeletonize.topostatsSkeletonize method) E edge_detection_method (topostats.grainstats.GrainStats attribute) entry_point() (in module topostats.entry_point) error (topostats.tracing.nodestats.NodeDict attribute) extract_height_profile (topostats.grainstats.GrainStats attribute) F feret module figsize (topostats.plotting.TopoSum attribute) filename (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) (topostats.io.LoadScans attribute) (topostats.plottingfuncs.Images attribute) (topostats.tracing.disordered_tracing.disorderedTrace attribute) (topostats.tracing.nodestats.nodeStats attribute) (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) fill_holes() (topostats.tracing.nodestats.nodeStats static method) filter_image() (topostats.filters.Filters method) filter_segments() (topostats.tracing.pruning.heightPruning method) Filters (class in topostats.filters) filters() (in module topostats.run_modules) final_skeletonisation_iteration() (topostats.tracing.skeletonize.topostatsSkeletonize method) find_best_next_point() (topostats.tracing.tracingfuncs.genTracingFuncs static method) find_branch_starts() (topostats.tracing.nodestats.nodeStats static method) find_branches_for_nodes() (in module geometry) find_cartesian_extremes() (topostats.grainstats.GrainStats static method) find_connections() (in module topostats.tracing.disordered_tracing) find_files() (in module topostats.io) find_grains() (topostats.grains.Grains method) first_derivative (topostats.tracing.dnacurvature.Curvature attribute) flatten_multi_class_tensor() (topostats.grains.Grains static method) full_dict (topostats.tracing.nodestats.nodeStats attribute) fwhm (topostats.tracing.nodestats.MatchedBranch attribute) G gaussian() (topostats.tracing.nodestats.nodeStats static method) gaussian_filter() (topostats.filters.Filters method) gaussian_mode (topostats.filters.Filters attribute) gaussian_size (topostats.filters.Filters attribute) genTracingFuncs (class in topostats.tracing.tracingfuncs) geometry module get_angle() (topostats.grainstats.GrainStats static method) get_bounding_boxes() (topostats.grains.Grains method) get_cmap() (topostats.Colormap method) (topostats.theme.Colormap method) get_cropped_region() (topostats.grainstats.GrainStats method) get_data() (topostats.io.LoadScans method) get_date_time() (in module topostats.io) get_feret_from_labelim() (in module feret) get_feret_from_mask() (in module feret) get_individual_grain_crops() (topostats.grains.Grains static method) get_local_pixels_binary() (topostats.tracing.skeletonize.topostatsSkeletonize static method) get_mask() (in module topostats.utils) get_mols_img() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) get_multi_class_grain_bounding_boxes() (topostats.grains.Grains static method) get_node_stats() (topostats.tracing.nodestats.nodeStats method) get_ordered_branches_and_vectors() (topostats.tracing.nodestats.nodeStats static method) get_ordered_traces() (topostats.tracing.ordered_tracing.OrderedTraceTopostats static method) get_out_path() (in module topostats.io) get_out_paths() (in module topostats.processing) get_over_under_img() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) get_region_properties() (topostats.grains.Grains static method) get_relative_paths() (in module topostats.io) get_shift() (topostats.grainstats.GrainStats static method) get_skan_image() (in module topostats.tracing.disordered_tracing) get_skeleton() (topostats.tracing.skeletonize.getSkeleton method) get_splined_traces() (topostats.tracing.splining.splineTrace method) get_start_point() (topostats.grainstats.GrainStats method) get_thresholds() (in module topostats.utils) get_topology() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) get_trace_idxs() (topostats.tracing.ordered_tracing.OrderedTraceNodestats static method) get_trace_segment() (topostats.tracing.ordered_tracing.OrderedTraceNodestats static method) get_vector() (topostats.tracing.nodestats.nodeStats static method) getSkeleton (class in topostats.tracing.skeletonize) graham_scan() (topostats.grainstats.GrainStats method) grain (topostats.tracing.nodestats.ImageDict attribute) grain_anchor() (in module topostats.tracing.disordered_tracing) grain_masks (topostats.io.LoadScans attribute) GRAIN_STATS_COLUMNS (in module topostats.grainstats) grain_trace_data (topostats.io.LoadScans attribute) grain_tracing_stats (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) (topostats.tracing.ordered_tracing.OrderedTraceTopostats attribute) Grains (class in topostats.grains) grains() (in module topostats.run_modules) GrainStats (class in topostats.grainstats) grainstats (topostats.grains.Grains attribute) grainstats() (in module topostats.run_modules) graph_to_skeleton_image() (topostats.tracing.nodestats.nodeStats static method) gwyddion() (topostats.Colormap static method) (topostats.theme.Colormap static method) H hdf5_to_dict() (in module topostats.io) height_bias (topostats.tracing.skeletonize.getSkeleton attribute) (topostats.tracing.skeletonize.topostatsSkeletonize attribute) height_profiles module height_prune() (topostats.tracing.pruning.heightPruning method) height_threshold (topostats.tracing.pruning.heightPruning attribute) (topostats.tracing.pruning.topostatsPrune attribute) heightPruning (class in topostats.tracing.pruning) heights (topostats.tracing.nodestats.MatchedBranch attribute) highlight_node_centres() (topostats.tracing.nodestats.nodeStats method) hist (topostats.plotting.TopoSum attribute) histogram_bins (topostats.plottingfuncs.Images attribute) histogram_log_axis (topostats.plottingfuncs.Images attribute) hue (topostats.plotting.TopoSum attribute) hulls() (in module feret) I identify_writhes() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) image (topostats.grains.Grains attribute) (topostats.io.LoadScans attribute) (topostats.tracing.disordered_tracing.disorderedTrace attribute) (topostats.tracing.nodestats.nodeStats attribute) (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) (topostats.tracing.ordered_tracing.OrderedTraceTopostats attribute) (topostats.tracing.pruning.heightPruning attribute) (topostats.tracing.skeletonize.getSkeleton attribute) (topostats.tracing.skeletonize.topostatsSkeletonize attribute) (topostats.tracing.splining.splineTrace attribute) image_dict (topostats.tracing.nodestats.nodeStats attribute) image_id (topostats.plotting.TopoSum attribute) image_name (topostats.grainstats.GrainStats attribute) image_set (topostats.plottingfuncs.Images attribute) image_statistics() (in module topostats.statistics) image_type (topostats.plottingfuncs.Images attribute) ImageDict (class in topostats.tracing.nodestats) Images (class in topostats.plottingfuncs) images (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) (topostats.tracing.ordered_tracing.OrderedTraceTopostats attribute) img (topostats.tracing.pruning.topostatsPrune attribute) img_dict (topostats.io.LoadScans attribute) img_idx_to_node (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) img_path (topostats.io.LoadScans attribute) img_paths (topostats.io.LoadScans attribute) improve_grain_segmentation_unet() (topostats.grains.Grains static method) interpolate_between_yvalue() (topostats.tracing.nodestats.nodeStats static method) interpolate_height_profile() (in module height_profiles) interpolation (topostats.plottingfuncs.Images attribute) iou_loss() (in module topostats.unet_masking) is_clockwise() (topostats.grainstats.GrainStats static method) J join_matching_branches_through_node() (topostats.tracing.nodestats.nodeStats static method) K kde (topostats.plotting.TopoSum attribute) keep_biggest_object() (topostats.tracing.nodestats.nodeStats static method) keep_largest_labelled_region() (topostats.grains.Grains static method) keep_largest_labelled_region_classes() (topostats.grains.Grains static method) L label (topostats.plotting.TopoSum attribute) label_branches() (topostats.tracing.pruning.heightPruning method) label_regions() (topostats.grains.Grains static method) labelled_data (topostats.grainstats.GrainStats attribute) lin_interp() (topostats.tracing.nodestats.nodeStats static method) linear_or_circular() (in module topostats.tracing.ordered_tracing) linearTrace() (topostats.tracing.tracingfuncs.reorderTrace static method) load_array() (in module topostats.io) load_asd() (topostats.io.LoadScans method) load_gwy() (topostats.io.LoadScans method) load_ibw() (topostats.io.LoadScans method) load_jpk() (topostats.io.LoadScans method) load_mplstyle() (in module topostats.plottingfuncs) load_pkl() (in module topostats.io) load_spm() (topostats.io.LoadScans method) load_topostats() (topostats.io.LoadScans method) LoadScans (class in topostats.io) local_area_sum() (in module topostats.tracing.pruning) (in module topostats.tracing.tracingfuncs) local_curvature (topostats.tracing.dnacurvature.Curvature attribute) LOG_ERROR_FORMATTER (in module topostats.logs.logs) LOG_INFO_FORMATTER (in module topostats.logs.logs) LOGGER (in module curvature) (in module feret) (in module height_profiles) (in module topostats) (in module topostats.filters) (in module topostats.grains) (in module topostats.grainstats) (in module topostats.io) (in module topostats.plotting) (in module topostats.plottingfuncs) (in module topostats.processing) (in module topostats.run_modules) (in module topostats.scars) (in module topostats.statistics) (in module topostats.theme) (in module topostats.thresholds) (in module topostats.tracing.disordered_tracing) (in module topostats.tracing.dnacurvature) (in module topostats.tracing.nodestats) (in module topostats.tracing.ordered_tracing) (in module topostats.tracing.pruning) (in module topostats.tracing.skeletonize) (in module topostats.tracing.splining) (in module topostats.unet_masking) (in module topostats.utils) (in module topostats.validation) LOGGER_NAME (in module topostats.logs.logs) M make_bounding_box_square() (in module topostats.unet_masking) make_grid() (topostats.tracing.tracingfuncs.genTracingFuncs static method) mask (topostats.tracing.disordered_tracing.disorderedTrace attribute) (topostats.tracing.nodestats.nodeStats attribute) (topostats.tracing.skeletonize.getSkeleton attribute) (topostats.tracing.skeletonize.topostatsSkeletonize attribute) mask_cmap (topostats.plottingfuncs.Images attribute) mask_smoothing_params (topostats.tracing.disordered_tracing.disorderedTrace attribute) masked_array (topostats.plottingfuncs.Images attribute) MatchedBranch (class in topostats.tracing.nodestats) max_length (topostats.tracing.pruning.heightPruning attribute) (topostats.tracing.pruning.topostatsPrune attribute) mean_iou() (in module topostats.unet_masking) measure_contour_length() (in module topostats.tracing.splining) measure_end_to_end_distance() (in module topostats.tracing.splining) median_flatten() (topostats.filters.Filters method) medians (topostats.filters.Filters attribute) melt_data() (topostats.plotting.TopoSum static method) melted_data (topostats.plotting.TopoSum attribute) merge_classes() (topostats.grains.Grains static method) merge_mappings() (in module topostats.io) method (topostats.tracing.skeletonize.getSkeleton attribute) method_outlier (topostats.tracing.pruning.heightPruning attribute) (topostats.tracing.pruning.topostatsPrune attribute) method_values (topostats.tracing.pruning.heightPruning attribute) (topostats.tracing.pruning.topostatsPrune attribute) metre_scaling_factor (topostats.grainstats.GrainStats attribute) metrics (topostats.tracing.nodestats.nodeStats attribute) min_max_feret() (in module feret) min_skeleton_size (topostats.tracing.disordered_tracing.disorderedTrace attribute) minimum_bbox_size_px (topostats.grains.Grains attribute) minimum_crossing_confs() (topostats.tracing.nodestats.nodeStats static method) minimum_grain_size (topostats.grains.Grains attribute) minimum_grain_size_px (topostats.grains.Grains attribute) MINIMUM_IMAGE_SIZE (topostats.io.LoadScans attribute) module curvature feret geometry height_profiles topostats topostats.__main__ topostats.entry_point topostats.filters topostats.grains topostats.grainstats topostats.io topostats.logs topostats.logs.logs topostats.plotting topostats.plottingfuncs topostats.processing topostats.run_modules topostats.scars topostats.statistics topostats.theme topostats.thresholds topostats.tracing topostats.tracing.disordered_tracing topostats.tracing.dnacurvature topostats.tracing.nodestats topostats.tracing.ordered_tracing topostats.tracing.pruning topostats.tracing.skeletonize topostats.tracing.splining topostats.tracing.tracingfuncs topostats.unet_masking topostats.utils topostats.validation mol_coords (topostats.tracing.nodestats.nodeStats attribute) mol_is_circular (topostats.tracing.splining.splineTrace attribute) (topostats.tracing.splining.windowTrace attribute) mol_ordered_trace (topostats.tracing.splining.splineTrace attribute) (topostats.tracing.splining.windowTrace attribute) mol_tracing_stats (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) (topostats.tracing.ordered_tracing.OrderedTraceTopostats attribute) molecule_coordinates (topostats.tracing.dnacurvature.Curvature attribute) molecule_id (topostats.plotting.TopoSum attribute) MutableMappingType (in module topostats.io) N n_grain (topostats.tracing.disordered_tracing.disorderedTrace attribute) (topostats.tracing.nodestats.nodeStats attribute) n_points (topostats.tracing.dnacurvature.Curvature attribute) name (topostats.Colormap attribute) (topostats.theme.Colormap attribute) nanoscope() (topostats.Colormap static method) (topostats.theme.Colormap static method) node_centre_mask (topostats.tracing.nodestats.nodeStats attribute) node_coords (topostats.tracing.nodestats.NodeDict attribute) node_dicts (topostats.tracing.nodestats.nodeStats attribute) node_extend_dist (topostats.tracing.nodestats.nodeStats attribute) node_joining_length (topostats.tracing.nodestats.nodeStats attribute) NodeDict (class in topostats.tracing.nodestats) nodes (topostats.tracing.nodestats.ImageDict attribute) nodeStats (class in topostats.tracing.nodestats) nodestats() (in module topostats.run_modules) nodestats_dict (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) nodestats_image() (in module topostats.tracing.nodestats) num_ticks (topostats.plottingfuncs.Images attribute) O only_centre_branches() (topostats.tracing.nodestats.nodeStats static method) order_branch() (in module topostats.tracing.tracingfuncs) order_branch_from_end() (in module topostats.tracing.pruning) order_branch_from_start() (in module topostats.tracing.tracingfuncs) order_branches() (topostats.tracing.nodestats.nodeStats static method) order_from_end() (topostats.tracing.ordered_tracing.OrderedTraceNodestats static method) ordered_coordinates (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) ordered_coords (topostats.tracing.nodestats.MatchedBranch attribute) ordered_trace_mask() (in module topostats.tracing.ordered_tracing) ordered_tracing() (in module topostats.run_modules) ordered_tracing_image() (in module topostats.tracing.ordered_tracing) OrderedTraceNodestats (class in topostats.tracing.ordered_tracing) OrderedTraceTopostats (class in topostats.tracing.ordered_tracing) orientation() (in module feret) otsu_threshold_multiplier (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) output_dir (topostats.plotting.TopoSum attribute) (topostats.plottingfuncs.Images attribute) P p2 (topostats.tracing.skeletonize.topostatsSkeletonize attribute) p3 (topostats.tracing.skeletonize.topostatsSkeletonize attribute) p4 (topostats.tracing.skeletonize.topostatsSkeletonize attribute) p5 (topostats.tracing.skeletonize.topostatsSkeletonize attribute) p6 (topostats.tracing.skeletonize.topostatsSkeletonize attribute) p7 (topostats.tracing.skeletonize.topostatsSkeletonize attribute) p8 (topostats.tracing.skeletonize.topostatsSkeletonize attribute) p9 (topostats.tracing.skeletonize.topostatsSkeletonize attribute) pad_bounding_box() (in module topostats.tracing.disordered_tracing) (in module topostats.unet_masking) pair_angles() (topostats.tracing.nodestats.nodeStats static method) pair_odd_branches (topostats.tracing.nodestats.nodeStats attribute) pair_vectors() (topostats.tracing.nodestats.nodeStats static method) palette (topostats.plotting.TopoSum attribute) path_to_str() (in module topostats.io) pixel_to_nanometre_scaling (topostats.grainstats.GrainStats attribute) pixel_to_nm_scaling (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) (topostats.io.LoadScans attribute) (topostats.plottingfuncs.Images attribute) (topostats.tracing.disordered_tracing.disorderedTrace attribute) (topostats.tracing.nodestats.NodeDict attribute) (topostats.tracing.nodestats.nodeStats attribute) (topostats.tracing.pruning.topostatsPrune attribute) (topostats.tracing.splining.splineTrace attribute) (topostats.tracing.splining.windowTrace attribute) plot() (topostats.grainstats.GrainStats static method) plot_and_save() (topostats.plottingfuncs.Images method) plot_coords (topostats.plottingfuncs.Images attribute) plot_crossing_linetrace_halfmax() (in module topostats.plotting) plot_curvatures() (topostats.plottingfuncs.Images method) plot_curvatures_individual_grains() (topostats.plottingfuncs.Images method) plot_feret() (in module feret) plot_height_profiles() (in module topostats.plotting) plot_histogram_and_save() (topostats.plottingfuncs.Images method) plot_opts (topostats.grainstats.GrainStats attribute) PLOTTING_SCHEMA (in module topostats.validation) pool_trace_circular() (topostats.tracing.splining.windowTrace static method) pool_trace_linear() (topostats.tracing.splining.windowTrace static method) predict_unet() (in module topostats.unet_masking) prep_arrays() (in module topostats.tracing.disordered_tracing) process() (in module topostats.run_modules) process_scan() (in module topostats.processing) profiles (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) prune_skeleton() (in module topostats.tracing.pruning) (topostats.tracing.pruning.topostatsPrune method) pruned_skeleton (topostats.tracing.disordered_tracing.disorderedTrace attribute) pruning_params (topostats.tracing.disordered_tracing.disorderedTrace attribute) R re_add_holes() (topostats.tracing.disordered_tracing.disorderedTrace method) read_64d() (in module topostats.io) read_char() (in module topostats.io) read_gwy_component_dtype() (in module topostats.io) read_null_terminated_string() (in module topostats.io) read_u32i() (in module topostats.io) read_yaml() (in module topostats.io) recip() (topostats.tracing.nodestats.nodeStats static method) reconcile_config_args() (in module topostats.run_modules) reduce_rows() (topostats.tracing.ordered_tracing.OrderedTraceNodestats static method) region_properties (topostats.grains.Grains attribute) (topostats.plottingfuncs.Images attribute) release (in module topostats) remove_common_values() (topostats.tracing.ordered_tracing.OrderedTraceNodestats static method) remove_duplicate_consecutive_tuples() (topostats.tracing.splining.splineTrace static method) remove_edge_intersecting_grains (topostats.grains.Grains attribute) remove_noise() (topostats.grains.Grains method) remove_nonlinear_polynomial() (topostats.filters.Filters method) remove_objects_too_small_to_process() (topostats.grains.Grains method) remove_quadratic() (topostats.filters.Filters method) remove_scars() (in module topostats.scars) remove_scars_config (topostats.filters.Filters attribute) remove_small_objects() (topostats.grains.Grains method) remove_tilt() (topostats.filters.Filters method) remove_touching_edge() (topostats.tracing.disordered_tracing.disorderedTrace static method) reorderTrace (class in topostats.tracing.tracingfuncs) ResolutionError results (topostats.filters.Filters attribute) return_points_in_array() (topostats.tracing.tracingfuncs.genTracingFuncs static method) rm_nibs() (in module topostats.tracing.pruning) rolling_window_size (topostats.tracing.splining.windowTrace attribute) rotating_calipers() (in module feret) roughness_rms() (in module topostats.statistics) row_alignment_quantile (topostats.filters.Filters attribute) run_curvature_stats() (in module topostats.processing) run_disordered_tracing() (in module topostats.processing) run_filters() (in module topostats.processing) run_grains() (in module topostats.processing) run_grainstats() (in module topostats.processing) run_nodestats() (in module topostats.processing) run_nodestats_tracing() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) run_ordered_tracing() (in module topostats.processing) run_spline_trace() (topostats.tracing.splining.splineTrace method) run_splining() (in module topostats.processing) run_topostats_tracing() (topostats.tracing.ordered_tracing.OrderedTraceTopostats method) run_toposum() (in module topostats.plotting) run_window_trace() (topostats.tracing.splining.windowTrace method) S save (topostats.plottingfuncs.Images attribute) save_array() (in module topostats.io) save_figure() (topostats.plottingfuncs.Images method) save_folder_grainstats() (in module topostats.io) save_pkl() (in module topostats.io) save_plot() (topostats.plotting.TopoSum method) save_topostats_file() (in module topostats.io) savefig_dpi (topostats.plottingfuncs.Images attribute) savefig_format (topostats.plotting.TopoSum attribute) (topostats.plottingfuncs.Images attribute) second_derivative (topostats.tracing.dnacurvature.Curvature attribute) segment_heights() (in module topostats.tracing.disordered_tracing) segment_middles() (in module topostats.tracing.disordered_tracing) segment_skeleton() (topostats.tracing.pruning.heightPruning method) set_cmap() (topostats.Colormap method) (topostats.theme.Colormap method) set_n_ticks() (in module topostats.plottingfuncs) set_palette() (topostats.plotting.TopoSum method) set_xlim() (topostats.plotting.TopoSum method) setup_logger() (in module topostats) (in module topostats.logs.logs) skeleton (topostats.tracing.disordered_tracing.disorderedTrace attribute) (topostats.tracing.nodestats.nodeStats attribute) (topostats.tracing.ordered_tracing.OrderedTraceNodestats attribute) (topostats.tracing.ordered_tracing.OrderedTraceTopostats attribute) (topostats.tracing.pruning.heightPruning attribute) (topostats.tracing.pruning.topostatsPrune attribute) skeleton_branches (topostats.tracing.pruning.heightPruning attribute) skeleton_branches_labelled (topostats.tracing.pruning.heightPruning attribute) skeleton_converged (topostats.tracing.skeletonize.topostatsSkeletonize attribute) skeleton_convolved (topostats.tracing.pruning.heightPruning attribute) skeleton_image_to_graph() (topostats.tracing.nodestats.nodeStats static method) skeleton_pruned (topostats.tracing.pruning.heightPruning attribute) skeletonisation_params (topostats.tracing.disordered_tracing.disorderedTrace attribute) smallest_grain_size_nm2 (topostats.grains.Grains attribute) smooth_mask() (topostats.tracing.disordered_tracing.disorderedTrace method) smoothed_mask (topostats.tracing.disordered_tracing.disorderedTrace attribute) (topostats.tracing.nodestats.nodeStats attribute) sns_plot() (topostats.plotting.TopoSum method) sns_violinplot() (topostats.plotting.TopoSum method) sort_and_shuffle() (topostats.tracing.skeletonize.topostatsSkeletonize static method) sort_clockwise() (in module feret) sort_coords() (in module feret) sort_points() (topostats.grainstats.GrainStats method) spline_circular_smoothing (topostats.tracing.splining.splineTrace attribute) spline_degree (topostats.tracing.splining.splineTrace attribute) spline_linear_smoothing (topostats.tracing.splining.splineTrace attribute) spline_step_size (topostats.tracing.splining.splineTrace attribute) splineTrace (class in topostats.tracing.splining) splining() (in module topostats.run_modules) splining_image() (in module topostats.tracing.splining) start (in module topostats.logs.logs) start_point (topostats.grainstats.GrainStats attribute) stat (topostats.plotting.TopoSum attribute) stat_to_sum (topostats.plotting.TopoSum attribute) summary_data (topostats.plotting.TopoSum attribute) SUMMARY_SCHEMA (in module topostats.validation) T threshold() (in module topostats.thresholds) threshold_absolute (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) threshold_method (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) threshold_std_dev (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) thresholds (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) tidy_border() (topostats.grains.Grains method) tidy_branches() (topostats.tracing.nodestats.nodeStats method) title (topostats.plottingfuncs.Images attribute) topostats module topostats.__main__ module topostats.entry_point module topostats.filters module topostats.grains module topostats.grainstats module topostats.io module topostats.logs module topostats.logs.logs module topostats.plotting module topostats.plottingfuncs module topostats.processing module topostats.run_modules module topostats.scars module topostats.statistics module topostats.theme module topostats.thresholds module topostats.tracing module topostats.tracing.disordered_tracing module topostats.tracing.dnacurvature module topostats.tracing.nodestats module topostats.tracing.ordered_tracing module topostats.tracing.pruning module topostats.tracing.skeletonize module topostats.tracing.splining module topostats.tracing.tracingfuncs module topostats.unet_masking module topostats.utils module topostats.validation module topostatsPrune (class in topostats.tracing.pruning) topostatsSkeletonize (class in topostats.tracing.skeletonize) TopoSum (class in topostats.plotting) toposum() (in module topostats.plotting) trace() (topostats.tracing.ordered_tracing.OrderedTraceNodestats method) trace_dna() (topostats.tracing.disordered_tracing.disorderedTrace method) trace_image_disordered() (in module topostats.tracing.disordered_tracing) tracing_stats (topostats.tracing.splining.splineTrace attribute) (topostats.tracing.splining.windowTrace attribute) triangle_height() (in module feret) U unet_config (topostats.grains.Grains attribute) update_background_class() (topostats.grains.Grains static method) update_config() (in module topostats.utils) update_plotting_config() (in module topostats.utils) V validate_config() (in module topostats.validation) var_to_label (topostats.plotting.TopoSum attribute) vet_class_connection_points() (topostats.grains.Grains static method) vet_class_sizes_single_grain() (topostats.grains.Grains static method) vet_grains() (topostats.grains.Grains static method) vet_numbers_of_regions_single_grain() (topostats.grains.Grains static method) vetting (topostats.grains.Grains attribute) visuals (topostats.tracing.nodestats.nodeStats attribute) W whole_skel_graph (topostats.tracing.nodestats.nodeStats attribute) windowTrace (class in topostats.tracing.splining) write_config_with_comments() (in module topostats.io) write_yaml() (in module topostats.io) writhe_direction() (topostats.tracing.ordered_tracing.OrderedTraceNodestats static method) Z zrange (topostats.plottingfuncs.Images attribute)