Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | Z _ __str__() (topostats.theme.Colormap method) __version__ (in module topostats) _binaryFinalThinCheck_a() (topostats.tracing.tracingfuncs.getSkeleton method) _binaryFinalThinCheck_b() (topostats.tracing.tracingfuncs.getSkeleton method) _binaryThinCheck_a() (topostats.tracing.tracingfuncs.getSkeleton method) _binaryThinCheck_b() (topostats.tracing.tracingfuncs.getSkeleton method) _binaryThinCheck_b_returncount() (topostats.tracing.tracingfuncs.getSkeleton method) _binaryThinCheck_c() (topostats.tracing.tracingfuncs.getSkeleton method) _binaryThinCheck_csharp() (topostats.tracing.tracingfuncs.getSkeleton method) _binaryThinCheck_d() (topostats.tracing.tracingfuncs.getSkeleton method) _binaryThinCheck_dsharp() (topostats.tracing.tracingfuncs.getSkeleton method) _calculate_centroid() (topostats.grainstats.GrainStats static method) _calculate_displacement() (topostats.grainstats.GrainStats static method) _calculate_radius() (topostats.grainstats.GrainStats static method) _checkForSaveDirectory() (topostats.tracing.dnatracing.dnaTrace method) _checkHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _checkWhichHeightPoints() (topostats.tracing.tracingfuncs.getSkeleton method) _condemnPoint() (topostats.tracing.tracingfuncs.getSkeleton method) _crop_array() (topostats.tracing.dnatracing.dnaTrace method) _deletePixelSubit1() (topostats.tracing.tracingfuncs.getSkeleton method) _deletePixelSubit2() (topostats.tracing.tracingfuncs.getSkeleton method) _deleteSquareEnds() (topostats.tracing.tracingfuncs.getSkeleton method) _doSkeletonisingIteration() (topostats.tracing.tracingfuncs.getSkeleton method) _extract_jpk() (topostats.io.LoadScan static method) _findBranchEnds() (topostats.tracing.tracingfuncs.getSkeleton method) _get_bounding_box() (topostats.tracing.dnatracing.dnaTrace method) _get_grain_array() (topostats.tracing.dnatracing.dnaTrace method) _get_mask() (in module topostats.utils) _get_skeletonize() (in module topostats.tracing.skeletonize) _get_threshold() (in module topostats.thresholds) _getDiaganolLeftDownwardHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _getDiaganolLeftUpwardHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _getDiaganolRightDownwardHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _getDiaganolRightUpwardHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _getHorizontalLeftHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _getHorizontalRightHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _getVerticalDonwardHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _getVerticalUpwardHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _ibw_pixel_to_nm_scaling() (topostats.io.LoadScan method) _identifyHighestPoint() (topostats.tracing.tracingfuncs.getSkeleton method) _initialiseHeightFindingDict() (topostats.tracing.tracingfuncs.getSkeleton method) _skeletonize_lee() (in module topostats.tracing.skeletonize) _skeletonize_medial_axis() (in module topostats.tracing.skeletonize) _skeletonize_thin() (in module topostats.tracing.skeletonize) _skeletonize_zhang() (in module topostats.tracing.skeletonize) _spm_pixel_to_nm_scaling() (topostats.io.LoadScan method) _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 absolute_area_threshold (topostats.grains.Grains attribute) absolute_smallest_grain_size (topostats.grains.Grains attribute) add_bounding_boxes_to_plot() (in module topostats.plottingfuncs), [1] add_pixel_to_nm_to_plotting_config() (in module topostats.plottingfuncs) add_to_dict() (topostats.io.LoadScans method) ALL_STATISTICS_COLUMNS (in module topostats.utils) area_thresholding() (topostats.grains.Grains method), [1] assemble_grain_mask_tensor_from_crops() (topostats.grains.Grains static method) average_background() (topostats.filters.Filters method), [1] average_height (topostats.tracing.tracingfuncs.getSkeleton attribute) axes (topostats.plottingfuncs.Images attribute) B base_output_dir (topostats.grainstats.GrainStats attribute) binary_map (topostats.tracing.tracingfuncs.getSkeleton attribute) bins (in module topostats.plotting) bound_padded_coordinates_to_image() (in module topostats.utils) bounding_boxes (topostats.grains.Grains attribute) C calc_diff() (topostats.filters.Filters static method), [1] calc_gradient() (topostats.filters.Filters method), [1] calc_minimum_grain_size() (topostats.grains.Grains method), [1] calculate_aspect_ratio() (topostats.grainstats.GrainStats method), [1] calculate_edges() (topostats.grainstats.GrainStats static method), [1] calculate_points() (topostats.grainstats.GrainStats static method), [1] calculate_radius_stats() (topostats.grainstats.GrainStats method), [1] calculate_region_connection_regions() (topostats.grains.Grains static method) calculate_squared_distance() (topostats.grainstats.GrainStats method), [1] calculate_stats() (topostats.grainstats.GrainStats method), [1] channel (topostats.io.LoadScan attribute) channel_data (topostats.io.LoadScan attribute) checkVectorsCandidatePoints() (topostats.tracing.tracingfuncs.genTracingFuncs static method) circularTrace() (topostats.tracing.tracingfuncs.reorderTrace static method) circularTrace_old() (topostats.tracing.tracingfuncs.reorderTrace static method) cmap (topostats.plottingfuncs.Images attribute) (topostats.theme.Colormap attribute) colname2label (in module topostats.plotting) colorbar (topostats.plottingfuncs.Images attribute) Colormap (class in topostats.theme) colour_regions() (topostats.grains.Grains method), [1] computeStats() (in module topostats.plotting) contour_lengths (topostats.tracing.dnatracing.dnaTrace 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), [1] convex_hull() (topostats.grainstats.GrainStats method), [1] convolve_skeleton() (in module topostats.utils) coords_2_img() (in module topostats.utils) core_set (topostats.plottingfuncs.Images attribute) countandGetNeighbours() (topostats.tracing.tracingfuncs.genTracingFuncs static method) countNeighbours() (topostats.tracing.tracingfuncs.genTracingFuncs static method) create_empty_dataframe() (in module topostats.utils), [1] create_parser() (in module topostats.run_topostats) create_trace_stats() (topostats.tracing.dnatracing.traceStats method) cropped_size (topostats.grainstats.GrainStats attribute) curvature (topostats.tracing.dnatracing.dnaTrace attribute) D data (topostats.grainstats.GrainStats attribute) (topostats.plottingfuncs.Images attribute) data2 (topostats.plottingfuncs.Images attribute) dataunitconversion() (in module topostats.plotting) df (topostats.tracing.dnatracing.traceStats attribute) 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) dir_search (topostats.tracing.tracingfuncs.getSkeleton attribute) direction (topostats.grains.Grains attribute) (topostats.grainstats.GrainStats attribute) directions (topostats.grains.Grains attribute) disordered_trace (topostats.tracing.dnatracing.dnaTrace attribute) dna_masks (topostats.tracing.dnatracing.dnaTrace attribute) dnaTrace (class in topostats.tracing.dnatracing) doSkeletonising() (topostats.tracing.tracingfuncs.getSkeleton method) E end_to_end_distance (topostats.tracing.dnatracing.dnaTrace attribute) extension (in module topostats.plotting) F file_path (topostats.io.LoadScan attribute) filename (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) (topostats.io.LoadScan attribute) (topostats.plottingfuncs.Images attribute) (topostats.tracing.dnatracing.dnaTrace attribute) filter_image() (topostats.filters.Filters method), [1] Filters (class in topostats.filters), [1] finalSkeletonisationIteration() (topostats.tracing.tracingfuncs.getSkeleton method) find_cartesian_extremes() (topostats.grainstats.GrainStats static method), [1] find_curvature() (topostats.tracing.dnatracing.dnaTrace method) find_files() (in module topostats.io) find_grains() (topostats.grains.Grains method), [1] find_images() (in module topostats.utils) findBestNextPoint() (topostats.tracing.tracingfuncs.genTracingFuncs static method) findWrithe() (topostats.tracing.dnatracing.dnaTrace method) fitted_traces (topostats.tracing.dnatracing.dnaTrace attribute) flatten_multi_class_tensor() (topostats.grains.Grains static method) folder_grainstats() (in module topostats.utils) full_image_data (topostats.tracing.dnatracing.dnaTrace attribute) G gauss_image (topostats.tracing.dnatracing.dnaTrace attribute) gaussian_filter() (topostats.filters.Filters method), [1] (topostats.tracing.dnatracing.dnaTrace method) gaussian_mode (topostats.filters.Filters attribute) gaussian_size (topostats.filters.Filters attribute) genTracingFuncs (class in topostats.tracing.tracingfuncs) get_angle() (topostats.grainstats.GrainStats static method), [1] get_bounding_boxes() (topostats.grains.Grains method), [1] get_cmap() (topostats.theme.Colormap method) get_config() (in module topostats._version) get_cropped_region() (topostats.grainstats.GrainStats method), [1] get_data() (topostats.io.LoadScan method) (topostats.io.LoadScans method) get_date_time() (in module topostats.io) get_disordered_trace() (topostats.tracing.dnatracing.dnaTrace method) get_fitted_traces() (topostats.tracing.dnatracing.dnaTrace method) get_individual_grain_crops() (topostats.grains.Grains static method) get_keywords() (in module topostats._version) get_mask() (in module topostats.utils), [1] get_max_min_ferets() (topostats.grainstats.GrainStats static method) get_multi_class_grain_bounding_boxes() (topostats.grains.Grains static method) get_numpy_arrays() (topostats.tracing.dnatracing.dnaTrace method) get_ordered_traces() (topostats.tracing.dnatracing.dnaTrace method) get_out_path() (in module topostats.io) (in module topostats.utils) get_region_properties() (topostats.grains.Grains static method), [1] get_relative_paths() (in module topostats.io) get_shift() (topostats.grainstats.GrainStats static method), [1] get_skeleton() (in module topostats.tracing.skeletonize) get_splined_traces() (topostats.tracing.dnatracing.dnaTrace method) get_start_point() (topostats.grainstats.GrainStats method), [1] get_thresholds() (in module topostats.utils), [1] get_triangle_height() (topostats.grainstats.GrainStats static method) get_versions() (in module topostats._version) getDNAmolHeightStats() (topostats.tracing.tracingfuncs.getSkeleton method) getLocalPixelsBinary() (topostats.tracing.tracingfuncs.genTracingFuncs static method) getNeighbours() (topostats.tracing.tracingfuncs.genTracingFuncs static method) getSkeleton (class in topostats.tracing.tracingfuncs) git_get_keywords() (in module topostats._version) git_pieces_from_vcs() (in module topostats._version) git_versions_from_keywords() (in module topostats._version) graham_scan() (topostats.grainstats.GrainStats method), [1] GRAIN_STATS_COLUMNS (in module topostats.grainstats) Grains (class in topostats.grains), [1] grains (topostats.tracing.dnatracing.dnaTrace attribute) grains_orig (topostats.tracing.dnatracing.dnaTrace attribute) GrainStats (class in topostats.grainstats), [1] grainstats (topostats.grains.Grains attribute) H HANDLERS (in module topostats._version) hdf5_to_dict() (in module topostats.io) highest_points (topostats.tracing.tracingfuncs.getSkeleton attribute) histogram_log_axis (topostats.plottingfuncs.Images attribute) I image (topostats.grains.Grains attribute) (topostats.io.LoadScan attribute) image_data (topostats.tracing.tracingfuncs.getSkeleton attribute) image_name (topostats.grainstats.GrainStats attribute) image_path (topostats.tracing.dnatracing.traceStats attribute) image_set (topostats.plottingfuncs.Images attribute) image_type (topostats.plottingfuncs.Images attribute) Images (class in topostats.plottingfuncs), [1] images (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) img_path (topostats.io.LoadScan attribute) importfromfile() (in module topostats.plotting) improve_grain_segmentation_unet() (topostats.grains.Grains static method) interpolation (topostats.plottingfuncs.Images attribute) is_clockwise() (topostats.grainstats.GrainStats static method), [1] K keep_largest_labelled_region() (topostats.grains.Grains static method) keep_largest_labelled_region_classes() (topostats.grains.Grains static method) L label_regions() (topostats.grains.Grains method) (topostats.grains.Grains static method) labelled_data (topostats.grainstats.GrainStats attribute) labelunitconversion() (in module topostats.plotting) linear_or_circular() (topostats.tracing.dnatracing.dnaTrace method) 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.LoadScan method) (topostats.io.LoadScans method) load_jpk() (topostats.io.LoadScan method) (topostats.io.LoadScans method) load_mplstyle() (in module topostats.plottingfuncs) load_pkl() (in module topostats.io) load_spm() (topostats.io.LoadScan method) (topostats.io.LoadScans method) load_topostats() (topostats.io.LoadScans method) LoadScan (class in topostats.io) LoadScans (class in topostats.io) LOG_CONFIG (in module topostats.logs.logs) LOG_ERROR_FORMATTER (in module topostats.logs.logs) LOG_FORMATTER (in module topostats.logs.logs) LOGGER (in module topostats) (in module topostats.filters) (in module topostats.grains) (in module topostats.grainstats) (in module topostats.io) (in module topostats.plottingfuncs) (in module topostats.run_topostats) (in module topostats.theme) (in module topostats.thresholds) (in module topostats.tracing.dnatracing) (in module topostats.tracing.skeletonize) (in module topostats.utils) (in module topostats.validation) LOGGER_NAME (in module topostats.logs.logs) LONG_VERSION_PY (in module topostats._version) loopedCircularTrace() (topostats.tracing.tracingfuncs.reorderTrace method) loopedLinearTrace() (topostats.tracing.tracingfuncs.reorderTrace method) M main() (in module topostats.run_topostats) makeGrid() (topostats.tracing.tracingfuncs.genTracingFuncs static method) mask_being_skeletonised (topostats.tracing.tracingfuncs.getSkeleton attribute) measure_contour_length() (topostats.tracing.dnatracing.dnaTrace method) measure_end_to_end_distance() (topostats.tracing.dnatracing.dnaTrace method) median_flatten() (topostats.filters.Filters method), [1] medians (topostats.filters.Filters attribute) merge_classes() (topostats.grains.Grains static method) merge_mappings() (in module topostats.io) minimum_grain_size (topostats.grains.Grains attribute) module topostats topostats.__main__ topostats._version topostats.filters, [1] topostats.grains, [1] topostats.grainstats, [1] topostats.io, [1] topostats.logs topostats.logs.logs topostats.plotting topostats.plottingfuncs, [1] topostats.run_topostats topostats.theme topostats.thresholds topostats.tracing topostats.tracing.dnatracing topostats.tracing.skeletonize topostats.tracing.tracingfuncs topostats.utils, [1] topostats.validation mol_is_circular (topostats.tracing.dnatracing.dnaTrace attribute) N name (topostats.theme.Colormap attribute) nanoscope() (topostats.theme.Colormap static method) neighbours (topostats.tracing.dnatracing.dnaTrace attribute) NotThisMethod num_circular (topostats.tracing.dnatracing.dnaTrace attribute) num_linear (topostats.tracing.dnatracing.dnaTrace attribute) number_of_columns (topostats.tracing.dnatracing.dnaTrace attribute) (topostats.tracing.tracingfuncs.getSkeleton attribute) number_of_rows (topostats.tracing.dnatracing.dnaTrace attribute) (topostats.tracing.tracingfuncs.getSkeleton attribute) number_of_traces (topostats.tracing.dnatracing.dnaTrace attribute) O ordered_traces (topostats.tracing.dnatracing.dnaTrace attribute) otsu_threshold_multiplier (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) output_dir (topostats.plottingfuncs.Images attribute) output_skeleton (topostats.tracing.tracingfuncs.getSkeleton attribute) P p2 (topostats.tracing.tracingfuncs.getSkeleton attribute) p3 (topostats.tracing.tracingfuncs.getSkeleton attribute) p4 (topostats.tracing.tracingfuncs.getSkeleton attribute) p5 (topostats.tracing.tracingfuncs.getSkeleton attribute) p6 (topostats.tracing.tracingfuncs.getSkeleton attribute) p7 (topostats.tracing.tracingfuncs.getSkeleton attribute) p8 (topostats.tracing.tracingfuncs.getSkeleton attribute) path_to_str() (in module topostats.io) pathman() (in module topostats.plotting) pep440_split_post() (in module topostats._version) pixel_size (topostats.tracing.dnatracing.dnaTrace attribute) (topostats.tracing.tracingfuncs.getSkeleton attribute) pixel_to_nanometre_scaling (topostats.grainstats.GrainStats attribute) pixel_to_nm_scaling (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) (topostats.io.LoadScan attribute) (topostats.plottingfuncs.Images attribute) plot() (topostats.grainstats.GrainStats static method), [1] plot_and_save() (topostats.plottingfuncs.Images method), [1] plot_curvatures() (topostats.plottingfuncs.Images method) plot_curvatures_individual_grains() (topostats.plottingfuncs.Images method) plot_histogram_and_save() (topostats.plottingfuncs.Images method), [1] plot_opts (topostats.grainstats.GrainStats attribute) plotCurvature() (topostats.tracing.dnatracing.dnaTrace method) plotdist() (in module topostats.plotting) plotdist2var() (in module topostats.plotting) plothist() (in module topostats.plotting) plothist2var() (in module topostats.plotting) plotjoint() (in module topostats.plotting) plotkde() (in module topostats.plotting) plotkde2var() (in module topostats.plotting) plotLinearVsCircular() (in module topostats.plotting) plotting_config (in module topostats.plotting) plotviolin() (in module topostats.plotting) plus_or_dot() (in module topostats._version) process_scan() (in module topostats.run_topostats) pruneSkeleton() (topostats.tracing.tracingfuncs.getSkeleton method) pruning (topostats.tracing.tracingfuncs.getSkeleton attribute) purge_obvious_crap() (topostats.tracing.dnatracing.dnaTrace method) R 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), [1] region_properties (topostats.grains.Grains attribute) (topostats.plottingfuncs.Images attribute) register_vcs_handler() (in module topostats._version) remove_noise() (topostats.grains.Grains method), [1] remove_nonlinear_polynomial() (topostats.filters.Filters method) remove_objects_too_small_to_process() (topostats.grains.Grains method) remove_quadratic() (topostats.filters.Filters method), [1] remove_small_objects() (topostats.grains.Grains method), [1] remove_tilt() (topostats.filters.Filters method), [1] render() (in module topostats._version) render_git_describe() (in module topostats._version) render_git_describe_long() (in module topostats._version) render_pep440() (in module topostats._version) render_pep440_branch() (in module topostats._version) render_pep440_old() (in module topostats._version) render_pep440_post() (in module topostats._version) render_pep440_post_branch() (in module topostats._version) render_pep440_pre() (in module topostats._version) reorderTrace (class in topostats.tracing.tracingfuncs) report_basic_stats() (topostats.tracing.dnatracing.dnaTrace method) ResolutionError results (topostats.filters.Filters attribute) returnPointsInArray() (topostats.tracing.tracingfuncs.genTracingFuncs static method) run_command() (in module topostats._version) S save (topostats.plottingfuncs.Images attribute) save_array() (in module topostats.io) save_array_figure() (topostats.plottingfuncs.Images method) save_cropped_grains (topostats.grainstats.GrainStats attribute) save_figure() (topostats.plottingfuncs.Images method), [1] save_folder_grainstats() (in module topostats.io) save_format (topostats.plottingfuncs.Images attribute) save_pkl() (in module topostats.io) save_topostats_file() (in module topostats.io) save_trace_stats() (topostats.tracing.dnatracing.traceStats method) saveCurvature() (topostats.tracing.dnatracing.dnaTrace method) savestats() (in module topostats.plotting) saveTraceFigures() (topostats.tracing.dnatracing.dnaTrace method) search_window (topostats.tracing.tracingfuncs.getSkeleton attribute) set() (topostats.theme.Colormap method) set_n_ticks() (in module topostats.plottingfuncs) setup_logger() (in module topostats) (in module topostats.logs.logs) show_traces() (topostats.tracing.dnatracing.dnaTrace method) sigma (topostats.tracing.dnatracing.dnaTrace attribute) skeleton_converged (topostats.tracing.tracingfuncs.getSkeleton attribute) skeletons (topostats.tracing.dnatracing.dnaTrace attribute) sort_points() (topostats.grainstats.GrainStats method), [1] splined_traces (topostats.tracing.dnatracing.dnaTrace attribute) start (in module topostats.logs.logs) start_point (topostats.grainstats.GrainStats attribute) suffix (topostats.io.LoadScan attribute) 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), [1] title (topostats.plottingfuncs.Images attribute) topostats module topostats.__main__ module topostats._version module topostats.filters module, [1] topostats.grains module, [1] topostats.grainstats module, [1] topostats.io module, [1] topostats.logs module topostats.logs.logs module topostats.plotting module topostats.plottingfuncs module, [1] topostats.run_topostats module topostats.theme module topostats.thresholds module topostats.tracing module topostats.tracing.dnatracing module topostats.tracing.skeletonize module topostats.tracing.tracingfuncs module topostats.utils module, [1] topostats.validation module trace_dna() (topostats.tracing.dnatracing.dnaTrace method) trace_object (topostats.tracing.dnatracing.traceStats attribute) traceStats (class in topostats.tracing.dnatracing) U update_background_class() (topostats.grains.Grains static method) update_config() (in module topostats.utils), [1] update_plotting_config() (in module topostats.utils) V validate_config() (in module topostats.validation) validate_plotting() (in module topostats.validation) VersioneerConfig (class in topostats._version) versions_from_parentdir() (in module topostats._version) 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) W write_config_with_comments() (in module topostats.io) write_yaml() (in module topostats.io), [1] writeContourLengths() (topostats.tracing.dnatracing.dnaTrace method) writeCoordinates() (topostats.tracing.dnatracing.dnaTrace method) Z zrange (topostats.plottingfuncs.Images attribute)