Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W _ __str__() (topostats.Colormap method) (topostats.theme.Colormap method) __version__ (in module topostats) _angle_between() (in module feret) _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_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) _checkForSaveDirectory() (topostats.tracing.dnatracing.dnaTrace method) _checkHeights() (topostats.tracing.tracingfuncs.getSkeleton method) _checkWhichHeightPoints() (topostats.tracing.tracingfuncs.getSkeleton method) _condemnPoint() (topostats.tracing.tracingfuncs.getSkeleton 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) _findBranchEnds() (topostats.tracing.tracingfuncs.getSkeleton 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) _gwy_print_dict() (topostats.io.LoadScans static method) _gwy_print_dict_wrapper() (topostats.io.LoadScans static method) _gwy_read_component() (topostats.io.LoadScans static method) _gwy_read_object() (topostats.io.LoadScans static method) _ibw_pixel_to_nm_scaling() (topostats.io.LoadScans method) _identifyHighestPoint() (topostats.tracing.tracingfuncs.getSkeleton method) _initialiseHeightFindingDict() (topostats.tracing.tracingfuncs.getSkeleton method) _jpk_pixel_to_nm_scaling() (topostats.io.LoadScans static method) _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) _remove_marked_scars() (in module topostats.scars) _remove_short_scars() (in module topostats.scars) _set_label() (topostats.plotting.TopoSum method) _setup_figure() (topostats.plotting.TopoSum method) _skeletonize_lee() (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.LoadScans 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 add_bounding_boxes_to_plot() (in module topostats.plottingfuncs) add_pixel_to_nm_to_plotting_config() (in module topostats.plottingfuncs) add_to_dict() (topostats.io.LoadScans method) adjust_coordinates() (in module topostats.tracing.dnatracing) all_pairs() (in module feret) ALL_STATISTICS_COLUMNS (in module topostats.utils) area_thresholding() (topostats.grains.Grains method) average_background() (topostats.filters.Filters method) B blu() (topostats.Colormap static method) (topostats.theme.Colormap static method) bound_padded_coordinates_to_image() (in module topostats.utils) C 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_derivatives() (topostats.tracing.dnacurvature.Curvature method) calculate_edges() (topostats.grainstats.GrainStats static method) calculate_points() (topostats.grainstats.GrainStats static method) calculate_radius_stats() (topostats.grainstats.GrainStats method) calculate_squared_distance() (topostats.grainstats.GrainStats method) calculate_stats() (topostats.grainstats.GrainStats method) check_run_steps() (in module topostats.processing) checkVectorsCandidatePoints() (topostats.tracing.tracingfuncs.genTracingFuncs static method) circularTrace() (topostats.tracing.tracingfuncs.reorderTrace static method) circularTrace_old() (topostats.tracing.tracingfuncs.reorderTrace static method) Colormap (class in topostats) (class in topostats.theme) colour_regions() (topostats.grains.Grains method) completion_message() (in module topostats.processing) CONFIG_DOCUMENTATION_REFERENCE (in module topostats.io) convert_basename_to_relative_paths() (in module topostats.io) convert_path() (in module topostats.utils) convex_hull() (topostats.grainstats.GrainStats method) coord_dist() (topostats.tracing.dnatracing.dnaTrace static method) countandGetNeighbours() (topostats.tracing.tracingfuncs.genTracingFuncs static method) countNeighbours() (topostats.tracing.tracingfuncs.genTracingFuncs static method) create_empty_dataframe() (in module topostats.utils) create_legacy_run_topostats_parser() (in module topostats.entry_point) create_legacy_toposum_parser() (in module topostats.entry_point) create_parser() (in module topostats.entry_point) crop_array() (in module topostats.tracing.dnatracing) Curvature (class in topostats.tracing.dnacurvature) D DEFAULT_CONFIG_SCHEMA (in module topostats.validation) dict_to_hdf5() (in module topostats.io) dilate_binary_image() (in module topostats.plottingfuncs) dnaTrace (class in topostats.tracing.dnatracing) doSkeletonising() (topostats.tracing.tracingfuncs.getSkeleton method) E entry_point() (in module topostats.entry_point) F feret module filter_image() (topostats.filters.Filters method) Filters (class in topostats.filters) finalSkeletonisationIteration() (topostats.tracing.tracingfuncs.getSkeleton method) find_cartesian_extremes() (topostats.grainstats.GrainStats static method) find_curvature() (topostats.tracing.dnatracing.dnaTrace method) find_files() (in module topostats.io) find_grains() (topostats.grains.Grains method) findBestNextPoint() (topostats.tracing.tracingfuncs.genTracingFuncs static method) G gaussian_filter() (topostats.filters.Filters method) (topostats.tracing.dnatracing.dnaTrace method) genTracingFuncs (class in topostats.tracing.tracingfuncs) 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_disordered_trace() (topostats.tracing.dnatracing.dnaTrace method) get_feret_from_labelim() (in module feret) get_feret_from_mask() (in module feret) get_fitted_traces() (topostats.tracing.dnatracing.dnaTrace method) get_mask() (in module topostats.utils) get_ordered_trace_cumulative_distances() (topostats.tracing.dnatracing.dnaTrace method) get_ordered_trace_heights() (topostats.tracing.dnatracing.dnaTrace method) get_ordered_traces() (topostats.tracing.dnatracing.dnaTrace method) get_out_path() (in module topostats.io) get_out_paths() (in module topostats.processing) get_region_properties() (topostats.grains.Grains static method) get_relative_paths() (in module topostats.io) get_shift() (topostats.grainstats.GrainStats static method) get_skeleton() (in module topostats.tracing.skeletonize) get_splined_traces() (topostats.tracing.dnatracing.dnaTrace method) get_start_point() (topostats.grainstats.GrainStats method) get_thresholds() (in module topostats.utils) 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) graham_scan() (topostats.grainstats.GrainStats method) grain_anchor() (in module topostats.tracing.dnatracing) GRAIN_STATS_COLUMNS (in module topostats.grainstats) Grains (class in topostats.grains) GrainStats (class in topostats.grainstats) gwyddion() (topostats.Colormap static method) (topostats.theme.Colormap static method) H hdf5_to_dict() (in module topostats.io) hulls() (in module feret) I image_statistics() (in module topostats.statistics) Images (class in topostats.plottingfuncs) is_clockwise() (topostats.grainstats.GrainStats static method) L label_regions() (topostats.grains.Grains method) legacy_run_topostats_entry_point() (in module topostats.entry_point) legacy_toposum_entry_point() (in module topostats.entry_point) 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.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) LOG_ERROR_FORMATTER (in module topostats.logs.logs) LOG_INFO_FORMATTER (in module topostats.logs.logs) LOGGER (in module feret) (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_topostats) (in module topostats.scars) (in module topostats.statistics) (in module topostats.theme) (in module topostats.thresholds) (in module topostats.tracing.dnacurvature) (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) loopedCircularTrace() (topostats.tracing.tracingfuncs.reorderTrace method) loopedLinearTrace() (topostats.tracing.tracingfuncs.reorderTrace method) M makeGrid() (topostats.tracing.tracingfuncs.genTracingFuncs static method) measure_contour_length() (topostats.tracing.dnatracing.dnaTrace method) measure_end_to_end_distance() (topostats.tracing.dnatracing.dnaTrace method) median_flatten() (topostats.filters.Filters method) melt_data() (topostats.plotting.TopoSum static method) min_max_feret() (in module feret) module feret 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_topostats topostats.scars topostats.statistics topostats.theme topostats.thresholds topostats.tracing topostats.tracing.dnacurvature topostats.tracing.dnatracing topostats.tracing.skeletonize topostats.tracing.tracingfuncs topostats.utils topostats.validation N nanoscope() (topostats.Colormap static method) (topostats.theme.Colormap static method) O orientation() (in module feret) P pad_bounding_box() (in module topostats.tracing.dnatracing) path_to_str() (in module topostats.io) plot() (topostats.grainstats.GrainStats static method) plot_and_save() (topostats.plottingfuncs.Images method) plot_feret() (in module feret) plot_histogram_and_save() (topostats.plottingfuncs.Images method) plotCurvature() (topostats.tracing.dnatracing.dnaTrace method) PLOTTING_SCHEMA (in module topostats.validation) prep_arrays() (in module topostats.tracing.dnatracing) process_scan() (in module topostats.processing) pruneSkeleton() (topostats.tracing.tracingfuncs.getSkeleton 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) release (in module topostats) remove_duplicate_consecutive_tuples() (topostats.tracing.dnatracing.dnaTrace static method) remove_noise() (topostats.grains.Grains method) remove_nonlinear_polynomial() (topostats.filters.Filters method) remove_quadratic() (topostats.filters.Filters method) remove_scars() (in module topostats.scars) remove_small_objects() (topostats.grains.Grains method) remove_tilt() (topostats.filters.Filters method) reorderTrace (class in topostats.tracing.tracingfuncs) returnPointsInArray() (topostats.tracing.tracingfuncs.genTracingFuncs static method) rotating_calipers() (in module feret) roughness_rms() (in module topostats.statistics) round_splined_traces() (in module topostats.tracing.dnatracing) run_dnatracing() (in module topostats.processing) run_filters() (in module topostats.processing) run_grains() (in module topostats.processing) run_grainstats() (in module topostats.processing) run_topostats() (in module topostats.run_topostats) run_toposum() (in module topostats.plotting) S 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) saveCurvature() (topostats.tracing.dnatracing.dnaTrace method) saveTraceFigures() (topostats.tracing.dnatracing.dnaTrace 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) show_traces() (topostats.tracing.dnatracing.dnaTrace method) sns_plot() (topostats.plotting.TopoSum method) sns_violinplot() (topostats.plotting.TopoSum method) sort_clockwise() (in module feret) sort_coords() (in module feret) sort_points() (topostats.grainstats.GrainStats method) start (in module topostats.logs.logs) SUMMARY_SCHEMA (in module topostats.validation) T threshold() (in module topostats.thresholds) tidy_border() (topostats.grains.Grains method) 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_topostats module topostats.scars module topostats.statistics module topostats.theme module topostats.thresholds module topostats.tracing module topostats.tracing.dnacurvature module topostats.tracing.dnatracing module topostats.tracing.skeletonize module topostats.tracing.tracingfuncs module topostats.utils module topostats.validation module TopoSum (class in topostats.plotting) toposum() (in module topostats.plotting) trace_dna() (topostats.tracing.dnatracing.dnaTrace method) trace_grain() (in module topostats.tracing.dnatracing) trace_image() (in module topostats.tracing.dnatracing) trace_mask() (in module topostats.tracing.dnatracing) triangle_height() (in module feret) trim_array() (in module topostats.tracing.dnatracing) U update_config() (in module topostats.utils) update_plotting_config() (in module topostats.utils) V validate_config() (in module topostats.validation) W write_config_with_comments() (in module topostats.io) write_yaml() (in module topostats.io)