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_local_curvature() (topostats.tracing.dnacurvature.Curvature method) _calculate_radius() (topostats.grainstats.GrainStats static method) _check_image_size() (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) _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) _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) _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) _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_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.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 absolute_area_threshold (topostats.grains.Grains attribute) add_bounding_boxes_to_plot() (in module topostats.plottingfuncs) add_to_dic() (topostats.io.LoadScans method) ALL_STATISTICS_COLUMNS (in module topostats.utils) alpha (topostats.plotting.TopoSum attribute) area_thresholding() (topostats.grains.Grains method) average_background() (topostats.filters.Filters method) average_height (topostats.tracing.tracingfuncs.getSkeleton attribute) axes (topostats.plottingfuncs.Images attribute) B base_dir (topostats.plotting.TopoSum attribute) base_output_dir (topostats.grainstats.GrainStats attribute) binary_map (topostats.tracing.tracingfuncs.getSkeleton attribute) bins (topostats.plotting.TopoSum attribute) blu() (topostats.theme.Colormap static method) bounding_boxes (topostats.grains.Grains attribute) 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) channel (topostats.io.LoadScans attribute) channel_data (topostats.io.LoadScans attribute) check_run_steps() (in module topostats.processing) checkVectorsCandidatePoints() (topostats.tracing.tracingfuncs.genTracingFuncs static method) circular (topostats.tracing.dnacurvature.Curvature attribute) circularTrace() (topostats.tracing.tracingfuncs.reorderTrace static method) circularTrace_old() (topostats.tracing.tracingfuncs.reorderTrace static method) cmap (topostats.plottingfuncs.Images attribute) (topostats.theme.Colormap attribute) colorbar (topostats.plottingfuncs.Images attribute) Colormap (class in topostats.theme) colour_regions() (topostats.grains.Grains method) completion_message() (in module topostats.processing) contour_lengths (topostats.tracing.dnatracing.dnaTrace attribute) convert_path() (in module topostats.utils) convex_hull() (topostats.grainstats.GrainStats method) 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) create_parser() (in module topostats.plotting) (in module topostats.run_topostats) create_trace_stats() (topostats.tracing.dnatracing.traceStats method) cropped_size (topostats.grainstats.GrainStats attribute) Curvature (class in topostats.tracing.dnacurvature) curvature (topostats.tracing.dnatracing.dnaTrace attribute) 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) (topostats.tracing.dnatracing.traceStats attribute) 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) dpi (topostats.plottingfuncs.Images attribute) E edge_detection_method (topostats.grainstats.GrainStats attribute) end_to_end_distance (topostats.tracing.dnatracing.dnaTrace attribute) F figsize (topostats.plotting.TopoSum attribute) file_ext (topostats.plotting.TopoSum attribute) filename (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) (topostats.io.LoadScans attribute) (topostats.plottingfuncs.Images attribute) (topostats.tracing.dnatracing.dnaTrace attribute) 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) findWrithe() (topostats.tracing.dnatracing.dnaTrace method) first_derivative (topostats.tracing.dnacurvature.Curvature attribute) fitted_traces (topostats.tracing.dnatracing.dnaTrace attribute) full_image_data (topostats.tracing.dnatracing.dnaTrace attribute) G gauss_image (topostats.tracing.dnatracing.dnaTrace attribute) gaussian_filter() (topostats.filters.Filters method) (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) get_bounding_boxes() (topostats.grains.Grains method) get_cmap() (topostats.theme.Colormap method) get_cropped_region() (topostats.grainstats.GrainStats method) get_data() (topostats.io.LoadScans method) get_disordered_trace() (topostats.tracing.dnatracing.dnaTrace method) get_fitted_traces() (topostats.tracing.dnatracing.dnaTrace method) get_mask() (in module topostats.utils) get_max_min_ferets() (topostats.grainstats.GrainStats 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) get_region_properties() (topostats.grains.Grains static method) 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) get_triangle_height() (topostats.grainstats.GrainStats static method) 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_STATS_COLUMNS (in module topostats.grainstats) Grains (class in topostats.grains) grains (topostats.tracing.dnatracing.dnaTrace attribute) grains_orig (topostats.tracing.dnatracing.dnaTrace attribute) GrainStats (class in topostats.grainstats) grainstats (topostats.grains.Grains attribute) gwyddion() (topostats.theme.Colormap static method) H highest_points (topostats.tracing.tracingfuncs.getSkeleton attribute) hist (topostats.plotting.TopoSum attribute) histogram_bins (topostats.plottingfuncs.Images attribute) histogram_log_axis (topostats.plottingfuncs.Images attribute) I image (topostats.grains.Grains attribute) (topostats.io.LoadScans attribute) image_data (topostats.tracing.tracingfuncs.getSkeleton attribute) image_id (topostats.plotting.TopoSum 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) images (topostats.filters.Filters attribute) (topostats.grains.Grains attribute) img_dict (topostats.io.LoadScans attribute) img_path (topostats.io.LoadScans attribute) img_paths (topostats.io.LoadScans attribute) interpolation (topostats.plottingfuncs.Images attribute) is_clockwise() (topostats.grainstats.GrainStats static method) K kde (topostats.plotting.TopoSum attribute) L label (topostats.plotting.TopoSum attribute) label_regions() (topostats.grains.Grains method) labelled_data (topostats.grainstats.GrainStats attribute) linear_or_circular() (topostats.tracing.dnatracing.dnaTrace method) linearTrace() (topostats.tracing.tracingfuncs.reorderTrace static method) load_array() (in module topostats.io) load_gwy() (topostats.io.LoadScans method) load_ibw() (topostats.io.LoadScans method) load_jpk() (topostats.io.LoadScans method) load_pkl() (in module topostats.io) load_spm() (topostats.io.LoadScans method) LoadScans (class in topostats.io) 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 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.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 main() (in module topostats.plotting) (in module topostats.run_topostats) makeGrid() (topostats.tracing.tracingfuncs.genTracingFuncs static method) mask_being_skeletonised (topostats.tracing.tracingfuncs.getSkeleton attribute) mask_cmap (topostats.plottingfuncs.Images attribute) masked_array (topostats.plottingfuncs.Images 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) medians (topostats.filters.Filters attribute) melted_data (topostats.plotting.TopoSum attribute) metre_scaling_factor (topostats.grainstats.GrainStats attribute) min_skeleton_size (topostats.tracing.dnatracing.dnaTrace attribute) minimum_grain_size (topostats.grains.Grains attribute) MINIMUM_IMAGE_SIZE (topostats.io.LoadScans attribute) module topostats topostats.__main__ 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.theme topostats.thresholds topostats.tracing topostats.tracing.dnacurvature topostats.tracing.dnatracing topostats.tracing.skeletonize topostats.tracing.tracingfuncs topostats.utils topostats.validation mol_is_circular (topostats.tracing.dnatracing.dnaTrace attribute) molecule_coordinates (topostats.tracing.dnacurvature.Curvature attribute) molecule_id (topostats.plotting.TopoSum attribute) N n_points (topostats.tracing.dnacurvature.Curvature attribute) name (topostats.theme.Colormap attribute) nanoscope() (topostats.theme.Colormap static method) neighbours (topostats.tracing.dnatracing.dnaTrace attribute) 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.plotting.TopoSum attribute) (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) palette (topostats.plotting.TopoSum attribute) path_to_str() (in module topostats.io) 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.LoadScans attribute) (topostats.plottingfuncs.Images attribute) plot() (topostats.grainstats.GrainStats static method) plot_and_save() (topostats.plottingfuncs.Images method) plot_histogram_and_save() (topostats.plottingfuncs.Images method) plot_opts (topostats.grainstats.GrainStats attribute) plotCurvature() (topostats.tracing.dnatracing.dnaTrace method) PLOTTING_SCHEMA (in module topostats.validation) process_scan() (in module topostats.processing) 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) region_properties (topostats.grains.Grains attribute) (topostats.plottingfuncs.Images attribute) release (in module topostats) remove_noise() (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) reorderTrace (class in topostats.tracing.tracingfuncs) report_basic_stats() (topostats.tracing.dnatracing.dnaTrace method) results (topostats.filters.Filters attribute) returnPointsInArray() (topostats.tracing.tracingfuncs.genTracingFuncs static method) row_alignment_quantile (topostats.filters.Filters attribute) S save (topostats.plottingfuncs.Images attribute) save_array() (in module topostats.io) save_array_figure() (topostats.plottingfuncs.Images method) save_figure() (topostats.plottingfuncs.Images method) save_folder_grainstats() (in module topostats.io) save_format (topostats.plottingfuncs.Images attribute) save_pkl() (in module topostats.io) save_plot() (topostats.plotting.TopoSum method) save_trace_stats() (topostats.tracing.dnatracing.traceStats method) saveCurvature() (topostats.tracing.dnatracing.dnaTrace method) saveTraceFigures() (topostats.tracing.dnatracing.dnaTrace method) search_window (topostats.tracing.tracingfuncs.getSkeleton attribute) second_derivative (topostats.tracing.dnacurvature.Curvature attribute) set() (topostats.theme.Colormap method) 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) sigma (topostats.tracing.dnatracing.dnaTrace attribute) skeleton_converged (topostats.tracing.tracingfuncs.getSkeleton attribute) skeletons (topostats.tracing.dnatracing.dnaTrace attribute) smallest_grain_size_nm2 (topostats.grains.Grains attribute) sns_melt_data() (topostats.plotting.TopoSum method) sns_plot() (topostats.plotting.TopoSum method) sns_violinplot() (topostats.plotting.TopoSum method) sort_points() (topostats.grainstats.GrainStats method) splined_traces (topostats.tracing.dnatracing.dnaTrace attribute) start (in module topostats.logs.logs) start_point (topostats.grainstats.GrainStats attribute) stat (topostats.plotting.TopoSum attribute) stat_to_sum (topostats.plotting.TopoSum attribute) summarise_by_image() (topostats.plotting.TopoSum method) 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) title (topostats.plottingfuncs.Images attribute) topostats module topostats.__main__ 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.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_object (topostats.tracing.dnatracing.traceStats attribute) traceStats (class in topostats.tracing.dnatracing) U unprocessed_grains (topostats.tracing.dnatracing.dnaTrace attribute) 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) W write_yaml() (in module topostats.io) writeContourLengths() (topostats.tracing.dnatracing.dnaTrace method) writeCoordinates() (topostats.tracing.dnatracing.dnaTrace method) Z zrange (topostats.plottingfuncs.Images attribute)