Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | W | Z A adapt_original_entries() (cryocat.cryomotl.RelionMotl method) adapt_to_trimming() (cryocat.cryomotl.Motl method) add_chain_prefix() (in module cryocat.ribana) add_chain_suffix() (in module cryocat.ribana) add_gaussian() (in module cryocat.cryomask) add_occupancy() (in module cryocat.ribana) add_traced_info() (in module cryocat.ribana) analyze_rotations() (in module cryocat.pana) apply_rotation() (cryocat.cryomotl.Motl method) apply_tomo_rotation() (cryocat.cryomotl.Motl method) assign_class() (in module cryocat.ribana) assign_column() (cryocat.cryomotl.Motl method) assign_random_classes() (cryocat.cryomotl.Motl method) B bandpass() (in module cryocat.cryomap) bin() (in module cryocat.tiltstack) C calculate_conjugates() (in module cryocat.cryomap) calculate_flcf() (in module cryocat.cryomap) calculate_total_dose() (in module cryocat.tiltstack) calculate_total_dose_batch() (in module cryocat.tiltstack) check() (cryocat.starfileio.Token static method) check_data_consistency() (in module cryocat.wedgeutils) check_df_correct_format() (cryocat.cryomotl.Motl static method) check_df_type() (cryocat.cryomotl.Motl method) check_existing_tight_mask_values() (in module cryocat.pana) check_then_consume() (cryocat.starfileio.Token static method) clean_by_distance() (cryocat.cryomotl.Motl method) clean_by_otsu() (cryocat.cryomotl.Motl method) cluster_subunits_to_rings() (cryocat.structure.NPC method) columns (cryocat.cryomotl.StopgapMotl attribute) columns_v3_0 (cryocat.cryomotl.RelionMotl attribute) columns_v3_1 (cryocat.cryomotl.RelionMotl attribute) columns_v4 (cryocat.cryomotl.RelionMotl attribute) COMMENT (cryocat.starfileio.TokenType attribute) compute_alignment_statistics() (in module cryocat.sta) compute_center_peak_stats_and_profiles() (in module cryocat.pana) compute_ctf_1d() (in module cryocat.cryomap) compute_diameter() (cryocat.structure.NPC static method) compute_dist_maps_voxels() (in module cryocat.pana) compute_gaussian_threshold() (in module cryocat.tmana) compute_peak_shapes() (in module cryocat.pana) compute_rmse() (in module cryocat.mathutils) compute_scores_map_threshold_triangle() (in module cryocat.tmana) compute_sharp_mask_overlap() (in module cryocat.pana) compute_solidity() (in module cryocat.cryomask) consume() (cryocat.starfileio.Token static method) convert_angles_from_relion() (cryocat.cryomotl.RelionMotl method) convert_angles_to_relion() (cryocat.cryomotl.RelionMotl method) convert_color_scheme() (in module cryocat.visplot) convert_shifts() (cryocat.cryomotl.RelionMotl method) convert_to_motl() (cryocat.cryomotl.DynamoMotl method) (cryocat.cryomotl.EmMotl method) (cryocat.cryomotl.Motl method) (cryocat.cryomotl.RelionMotl method) (cryocat.cryomotl.StopgapMotl method) convert_to_radial() (in module cryocat.visplot) convert_to_sg_motl() (cryocat.cryomotl.StopgapMotl static method) convert_to_spherical() (in module cryocat.visplot) correct_bbox() (in module cryocat.pana) create_angular_distance_maps() (in module cryocat.tmana) create_denovo_multiref_run() (in module cryocat.sta) create_em_path() (in module cryocat.pana) create_empty_motl_df() (cryocat.cryomotl.Motl static method) create_final_output() (cryocat.cryomotl.RelionMotl method) create_multiref_run() (in module cryocat.sta) create_optics_group_v3_1() (cryocat.cryomotl.RelionMotl method) create_optics_group_v4() (cryocat.cryomotl.RelionMotl method) create_output_base_name() (in module cryocat.pana) create_output_folder_name() (in module cryocat.pana) create_output_folder_path() (in module cryocat.pana) create_particles_data() (cryocat.cryomotl.RelionMotl method) create_projection() (in module cryocat.visplot) create_relion_df() (cryocat.cryomotl.RelionMotl method) create_smooth_polar_histogram() (in module cryocat.visplot) create_starting_parameters_1D() (in module cryocat.tmana) create_starting_parameters_2D() (in module cryocat.tmana) create_structure_path() (in module cryocat.pana) create_subtomo_name() (in module cryocat.pana) create_subtomograms_for_tm() (in module cryocat.pana) create_summary_pdf() (in module cryocat.pana) create_tomo_name() (in module cryocat.pana) create_wedge_list_em_batch() (in module cryocat.wedgeutils) create_wedge_list_sg() (in module cryocat.wedgeutils) create_wedge_list_sg_batch() (in module cryocat.wedgeutils) create_wedge_names() (in module cryocat.pana) cryoCAT module cryocat.cryomap module cryocat.cryomask module cryocat.cryomotl module cryocat.ioutils module cryocat.mathutils module cryocat.mdoc module cryocat.nnana module cryocat.pana module cryocat.ribana module cryocat.sta module cryocat.starfileio module cryocat.structure module cryocat.tiltstack module cryocat.tmana module cryocat.visplot module cryocat.wedgeutils module ctffind4_read() (in module cryocat.ioutils) cut_the_best_subtomo() (in module cryocat.pana) cylindrical_mask() (in module cryocat.cryomask) D deconvolve() (in module cryocat.cryomap) default_version (cryocat.cryomotl.RelionMotl attribute) defocus_load() (in module cryocat.ioutils) difference() (in module cryocat.cryomask) dimensions_load() (in module cryocat.ioutils) dose_filter() (in module cryocat.tiltstack) dose_filter_single_image() (in module cryocat.tiltstack) drop_duplicates() (cryocat.cryomotl.Motl method) DynamoMotl (class in cryocat.cryomotl) E ellipsoid_mask() (in module cryocat.cryomask) em2mrc() (in module cryocat.cryomap) EmMotl (class in cryocat.cryomotl) emmotl2relion() (in module cryocat.cryomotl) emmotl2stopgap() (in module cryocat.cryomotl) equalize_histogram() (in module cryocat.tiltstack) evaluate_alignment() (in module cryocat.sta) evaluate_classification() (in module cryocat.sta) evaluate_multirun_stability() (in module cryocat.sta) evaluate_scores_map() (in module cryocat.tmana) extract_subvolume() (in module cryocat.cryomap) F fileformat_replace_pattern() (in module cryocat.ioutils) fill() (cryocat.cryomotl.Motl method) fill_hollow_mask() (in module cryocat.cryomask) fill_wedge() (in module cryocat.visplot) filter_dist_maps() (in module cryocat.tmana) flip() (in module cryocat.cryomap) flip_handedness() (cryocat.cryomotl.Motl method) G gctf_read() (in module cryocat.ioutils) get_all_pairs() (in module cryocat.mathutils) get_angles() (cryocat.cryomotl.Motl method) get_barycentric_motl() (cryocat.cryomotl.Motl method) get_bounding_box() (in module cryocat.cryomask) get_center_and_radius() (cryocat.structure.NPC static method) get_center_with_radius() (cryocat.structure.NPC static method) get_centers_as_motl() (cryocat.structure.NPC static method) get_central_label() (in module cryocat.tmana) get_central_plane_labels() (in module cryocat.tmana) get_chain_distances() (in module cryocat.ribana) get_class_occupancy() (in module cryocat.sta) get_class_polysome_occupancies_mdp() (in module cryocat.ribana) get_class_polysome_occupancies_mp() (in module cryocat.ribana) get_colors_from_palette() (in module cryocat.visplot) get_coordinates() (cryocat.cryomotl.Motl method) get_correct_format() (in module cryocat.cryomask) get_cross_slices() (in module cryocat.cryomap) get_data_from_warp_xml() (in module cryocat.ioutils) get_ellipsoid_label() (in module cryocat.tmana) get_feature() (cryocat.cryomotl.Motl method) get_feature_nn() (in module cryocat.ribana) get_feature_nn_indices() (in module cryocat.nnana) (in module cryocat.ribana) get_filename_from_path() (in module cryocat.ioutils) get_filter_radius() (in module cryocat.cryomap) get_frame_and_comments() (cryocat.starfileio.Starfile static method) get_image() (cryocat.mdoc.Mdoc method) get_image_by_zvalue() (cryocat.mdoc.Mdoc method) get_image_by_zvalue_range() (cryocat.mdoc.Mdoc method) get_image_feature() (cryocat.mdoc.Mdoc method) get_image_features() (cryocat.mdoc.Mdoc method) get_images() (cryocat.mdoc.Mdoc method) get_images_by_zvalue_ranges() (cryocat.mdoc.Mdoc method) get_images_by_zvalues() (cryocat.mdoc.Mdoc method) get_indices() (in module cryocat.pana) get_mask_stats() (in module cryocat.pana) get_mass_center() (in module cryocat.cryomask) get_mass_dimensions() (in module cryocat.cryomask) get_max_number_digits() (cryocat.cryomotl.Motl method) get_monosome_stats() (in module cryocat.ribana) get_motl_extension() (in module cryocat.sta) get_motl_intersection() (cryocat.cryomotl.Motl class method) get_motl_subset() (cryocat.cryomotl.Motl method) get_new_subunit_idx() (cryocat.structure.NPC static method) get_nn_dist() (in module cryocat.ribana) get_nn_distances() (in module cryocat.nnana) (in module cryocat.ribana) get_nn_rotations() (in module cryocat.nnana) (in module cryocat.ribana) get_nn_stats() (in module cryocat.nnana) (in module cryocat.ribana) get_nn_within_distance() (in module cryocat.nnana) get_nn_within_radius() (in module cryocat.nnana) get_number_of_digits() (in module cryocat.mathutils) get_number_of_lines_with_character() (in module cryocat.ioutils) get_polysome_stats() (in module cryocat.ribana) get_random_subset() (cryocat.cryomotl.Motl method) get_relative_position() (cryocat.cryomotl.Motl method) get_rotations() (cryocat.cryomotl.Motl method) (in module cryocat.ribana) get_shape_stats() (in module cryocat.pana) get_sharp_mask_stats() (in module cryocat.pana) get_similar_size_factors() (in module cryocat.mathutils) get_soft_mask_stats() (in module cryocat.pana) get_specifier_id() (cryocat.starfileio.Starfile static method) get_stable_particles() (in module cryocat.sta) get_start_end_indices() (in module cryocat.cryomap) get_subtomos_class_stability() (in module cryocat.sta) get_unique_values() (cryocat.cryomotl.Motl method) get_version_from_file() (cryocat.cryomotl.RelionMotl static method) get_version_specific_names() (cryocat.cryomotl.RelionMotl static method) H highpass() (in module cryocat.cryomap) I imod_com_read() (in module cryocat.ioutils) intersection() (in module cryocat.cryomask) is_float() (in module cryocat.ioutils) K keep_image() (cryocat.mdoc.Mdoc method) keep_images() (cryocat.mdoc.Mdoc method) kept_images() (cryocat.mdoc.Mdoc method) L LITERAL (cryocat.starfileio.TokenType attribute) load() (cryocat.cryomotl.Motl class method) lookahead() (cryocat.starfileio.Token static method) LOOP (cryocat.starfileio.TokenType attribute) lowpass() (in module cryocat.cryomap) M make_angles_canonical() (cryocat.cryomotl.Motl method) map_tight_mask() (in module cryocat.cryomask) mask_overlap() (in module cryocat.cryomask) Mdoc (class in cryocat.mdoc) merge_and_renumber() (cryocat.cryomotl.Motl class method) merge_rings() (cryocat.structure.NPC static method) merge_subunits() (cryocat.structure.NPC static method) ModMotl (class in cryocat.cryomotl) module cryoCAT cryocat.cryomap cryocat.cryomask cryocat.cryomotl cryocat.ioutils cryocat.mathutils cryocat.mdoc cryocat.nnana cryocat.pana cryocat.ribana cryocat.sta cryocat.starfileio cryocat.structure cryocat.tiltstack cryocat.tmana cryocat.visplot cryocat.wedgeutils molmap_tight_mask() (in module cryocat.cryomask) Motl (class in cryocat.cryomotl) motl_columns (cryocat.cryomotl.Motl attribute) mrc2em() (in module cryocat.cryomap) N NEWLINE (cryocat.starfileio.TokenType attribute) normalize() (in module cryocat.cryomap) normalize_under_mask() (in module cryocat.cryomap) NPC (class in cryocat.structure) O one_value_per_line_read() (in module cryocat.ioutils) otsu_threshold() (in module cryocat.mathutils) P pad() (in module cryocat.cryomap) pairs (cryocat.cryomotl.StopgapMotl attribute) parse_column() (cryocat.starfileio.Token static method) parse_columns() (cryocat.starfileio.Token static method) parse_newline_or_comments() (cryocat.starfileio.Token static method) parse_rows() (cryocat.starfileio.Token static method) parse_specifier() (cryocat.starfileio.Token static method) parse_subtomo_id() (cryocat.cryomotl.RelionMotl method) parse_tomo_id() (cryocat.cryomotl.RelionMotl method) pixels2resolution() (in module cryocat.cryomap) place_object() (in module cryocat.cryomap) plot_alignment_stability() (in module cryocat.visplot) plot_class_occupancy() (in module cryocat.visplot) plot_class_stability() (in module cryocat.visplot) plot_classification_convergence() (in module cryocat.visplot) plot_nn_coord() (in module cryocat.nnana) (in module cryocat.ribana) plot_nn_coord_df() (in module cryocat.nnana) (in module cryocat.ribana) plot_nn_rot_coord_df() (in module cryocat.nnana) (in module cryocat.ribana) plot_orientational_distribution() (in module cryocat.visplot) plot_polar_nn_distances() (in module cryocat.visplot) plot_scores_and_peaks() (in module cryocat.pana) postprocess() (in module cryocat.cryomask) prepare_optics_data() (cryocat.cryomotl.RelionMotl method) prepare_particles_data() (cryocat.cryomotl.RelionMotl method) preprocess_params() (in module cryocat.cryomask) project_equidistant() (in module cryocat.visplot) project_lambert() (in module cryocat.visplot) project_points_on_sphere() (in module cryocat.visplot) project_stereo() (in module cryocat.visplot) PROPERTY (cryocat.starfileio.TokenType attribute) R read() (cryocat.starfileio.Starfile static method) (in module cryocat.cryomap) read_hdf5() (in module cryocat.cryomap) read_in() (cryocat.cryomotl.DynamoMotl static method) (cryocat.cryomotl.EmMotl static method) (cryocat.cryomotl.ModMotl static method) (cryocat.cryomotl.RelionMotl method) (cryocat.cryomotl.StopgapMotl static method) recenter() (in module cryocat.cryomap) recenter_to_subparticle() (cryocat.cryomotl.Motl static method) recompute_dist_maps() (in module cryocat.pana) relion2emmotl() (in module cryocat.cryomotl) relion2stopgap() (in module cryocat.cryomotl) RelionMotl (class in cryocat.cryomotl) remove_feature() (cryocat.cryomotl.Motl method) remove_image() (cryocat.mdoc.Mdoc method) remove_images() (cryocat.mdoc.Mdoc method) remove_lines() (cryocat.starfileio.Starfile static method) (in module cryocat.ioutils) remove_out_of_bounds_particles() (cryocat.cryomotl.Motl method) removed_images() (cryocat.mdoc.Mdoc method) rename_folders() (in module cryocat.pana) rename_scores_angles() (in module cryocat.pana) renumber_objects_sequentially() (cryocat.cryomotl.Motl method) renumber_particles() (cryocat.cryomotl.Motl method) reorder_images() (cryocat.mdoc.Mdoc method) reset_images() (cryocat.mdoc.Mdoc method) resolution2pixels() (in module cryocat.cryomap) rotate() (in module cryocat.cryomap) (in module cryocat.cryomask) run_analysis() (in module cryocat.pana) run_angle_analysis() (in module cryocat.pana) S scale() (in module cryocat.cryomap) scale_coordinates() (cryocat.cryomotl.Motl method) scores_extract_particles() (in module cryocat.tmana) select_peaks() (in module cryocat.tmana) set_pixel_size() (cryocat.cryomotl.RelionMotl method) set_version() (cryocat.cryomotl.RelionMotl method) set_version_specific_names() (cryocat.cryomotl.RelionMotl method) sg_df_reset_index() (cryocat.cryomotl.StopgapMotl static method) shift() (in module cryocat.cryomap) shift2() (in module cryocat.cryomap) shift_positions() (cryocat.cryomotl.Motl method) shrink_full_mask() (in module cryocat.cryomask) sort_by_tilt() (cryocat.mdoc.Mdoc method) spherical_mask() (in module cryocat.cryomask) split_by_feature() (cryocat.cryomotl.Motl method) split_in_asymmetric_subunits() (cryocat.cryomotl.Motl method) Starfile (class in cryocat.starfileio) stopgap2emmotl() (in module cryocat.cryomotl) stopgap2relion() (in module cryocat.cryomotl) StopgapMotl (class in cryocat.cryomotl) subtraction() (in module cryocat.cryomask) suppress_warnings() (in module cryocat.tiltstack) T tlt_load() (in module cryocat.ioutils) Token (class in cryocat.starfileio) tokenize() (cryocat.starfileio.Token static method) TokenType (class in cryocat.starfileio) total_dose_load() (in module cryocat.ioutils) trace_chains() (in module cryocat.ribana) trim() (in module cryocat.cryomap) U unify_nn_orientations() (cryocat.structure.NPC static method) union() (in module cryocat.cryomask) update_coordinates() (cryocat.cryomotl.Motl method) W warp_ctf_read() (in module cryocat.ioutils) write() (cryocat.mdoc.Mdoc method) (cryocat.starfileio.Starfile static method) (in module cryocat.cryomap) write_hdf5() (in module cryocat.cryomap) write_out() (cryocat.cryomotl.DynamoMotl method) (cryocat.cryomotl.EmMotl method) (cryocat.cryomotl.Motl method) (cryocat.cryomotl.RelionMotl method) (cryocat.cryomotl.StopgapMotl method) (in module cryocat.cryomask) write_out_motl() (in module cryocat.sta) write_to_model_file() (cryocat.cryomotl.Motl method) Z z_shift_load() (in module cryocat.ioutils)