Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A adapt_original_entries() (cryocat.core.cryomotl.RelionMotl method) adapt_to_trimming() (cryocat.core.cryomotl.Motl method) add_chain_prefix() (in module cryocat.analysis.ribana) add_chain_suffix() (in module cryocat.analysis.ribana) add_field() (cryocat.core.mdoc.Mdoc method) add_gaussian() (in module cryocat.core.cryomask) add_noise() (cryocat.analysis.tango.Particle method) add_noise_and_project_to_so3() (cryocat.utils.geom.Matrix method) add_occupancy() (in module cryocat.analysis.ribana) add_traced_info() (in module cryocat.analysis.ribana) align_points_to_xy_plane() (in module cryocat.utils.geom) AlphaComplexDescriptor (class in cryocat.analysis.tango) analyze_rotations() (in module cryocat.analysis.pana) angle_between_n_vectors() (in module cryocat.utils.geom) angle_between_vectors() (in module cryocat.utils.geom) angular_distance() (in module cryocat.utils.geom) angular_score_for_c_symmetry() (in module cryocat.utils.geom) AngularScoreNN (class in cryocat.analysis.tango) AngularScoreStatsTwist (class in cryocat.analysis.tango) apply_defaults() (in module cryocat.analysis.visplot) apply_rotation() (cryocat.core.cryomotl.Motl method) apply_tomo_rotation() (cryocat.core.cryomotl.Motl method) apply_wedge_mask() (in module cryocat.utils.wedgeutils) area() (cryocat.utils.geom.Triangle method) area_triangle() (in module cryocat.utils.geom) assign_affiliation_distance_based() (cryocat.analysis.structure.PleomorphicSurface static method) assign_affiliation_intersection_based() (cryocat.analysis.structure.PleomorphicSurface static method) assign_affiliation_mask_based() (cryocat.analysis.structure.PleomorphicSurface static method) assign_class() (in module cryocat.analysis.ribana) assign_column() (cryocat.core.cryomotl.Motl method) assign_cone_ids_by_dot() (cryocat.analysis.tango.SHOTDescriptor method) assign_random_classes() (cryocat.core.cryomotl.Motl method) assign_shell_and_cone_ids() (cryocat.analysis.tango.SHOTDescriptor method) AxisRot (class in cryocat.analysis.tango) B bandpass() (in module cryocat.core.cryomap) BaseBuilder (class in cryocat.analysis.visplot) bin() (in module cryocat.core.tiltstack) binarize() (in module cryocat.core.cryomap) build_adjacency() (cryocat.analysis.memthick.MeshNormalVoter method) build_descriptor() (cryocat.analysis.tango.CustomDescriptor method) (cryocat.analysis.tango.Descriptor method) build_descriptor_feature_map() (cryocat.analysis.tango.Descriptor static method) build_feature_descriptor_map() (cryocat.analysis.tango.Descriptor static method) build_trace() (cryocat.analysis.visplot.BaseBuilder method) (cryocat.analysis.visplot.Hist2DBuilder method) (cryocat.analysis.visplot.HistBuilder method) (cryocat.analysis.visplot.KDEBuilder method) (cryocat.analysis.visplot.ScatterBuilder method) C calculate_conjugates() (in module cryocat.core.cryomap) calculate_flcf() (in module cryocat.core.cryomap) calculate_masked_fsc() (in module cryocat.core.cryomap) calculate_total_dose_batch() (in module cryocat.core.tiltstack) cartesian_to_spherical() (in module cryocat.utils.geom) Catalog (class in cryocat.analysis.tango) CentralAngleStatsAlphaComplex (class in cryocat.analysis.tango) CentralAngleStatsPLComplex (class in cryocat.analysis.tango) change_frame_path() (cryocat.core.mdoc.Mdoc method) change_handedness_coordinates() (in module cryocat.utils.geom) change_to_separate_graphs() (cryocat.analysis.visplot.BaseBuilder method) check() (cryocat.utils.starfileio.Token static method) check_data_consistency() (in module cryocat.utils.wedgeutils) check_df_correct_format() (cryocat.core.cryomotl.Motl static method) check_df_type() (cryocat.core.cryomotl.Motl method) check_existing_tight_mask_values() (in module cryocat.analysis.pana) check_isWarp() (cryocat.core.cryomotl.RelionMotlv5 method) check_then_consume() (cryocat.utils.starfileio.Token static method) circumcircle() (cryocat.utils.geom.Triangle method) circumcircle_radius() (cryocat.utils.geom.Triangle method) clean_by_distance() (cryocat.core.cryomotl.Motl method) clean_by_distance_to_points() (cryocat.core.cryomotl.Motl method) clean_by_normals() (cryocat.analysis.structure.PleomorphicSurface static method) clean_by_otsu() (cryocat.core.cryomotl.Motl method) clean_by_radius() (cryocat.analysis.structure.PleomorphicSurface static method) clean_by_tomo_mask() (cryocat.core.cryomotl.Motl method) clean_subtomo_name_column() (cryocat.core.cryomotl.RelionMotlv5 static method) clean_tomo_name_column() (cryocat.core.cryomotl.RelionMotlv5 static method) cluster_subunits_to_rings() (cryocat.analysis.structure.NPC method) colorscale (cryocat.analysis.visplot.Defaults attribute) colorway (cryocat.analysis.visplot.Defaults attribute) columns (cryocat.core.cryomotl.ModMotl attribute) (cryocat.core.cryomotl.StopgapMotl attribute) columns_v3_0 (cryocat.core.cryomotl.RelionMotl attribute) columns_v3_1 (cryocat.core.cryomotl.RelionMotl attribute) columns_v4 (cryocat.core.cryomotl.RelionMotl attribute) columns_v5 (cryocat.core.cryomotl.RelionMotlv5 attribute) columns_v5_1 (cryocat.core.cryomotl.RelionMotl attribute) columns_v5_centAng (cryocat.core.cryomotl.RelionMotlv5 attribute) COMMENT (cryocat.utils.starfileio.TokenType attribute) compare_rotations() (in module cryocat.utils.geom) compute() (cryocat.analysis.tango.AngularScoreStatsTwist method) (cryocat.analysis.tango.CentralAngleStatsAlphaComplex method) (cryocat.analysis.tango.CentralAngleStatsPLComplex method) (cryocat.analysis.tango.CountSHOT method) (cryocat.analysis.tango.DistProductStatsTwist method) (cryocat.analysis.tango.EuclideanDistStatsTwist method) (cryocat.analysis.tango.EulerCharAlphaComplex method) (cryocat.analysis.tango.Feature method) (cryocat.analysis.tango.GeodesicnDistStatsTwist method) (cryocat.analysis.tango.LinkTypeAlphaComplex method) (cryocat.analysis.tango.NNCountTwist method) (cryocat.analysis.tango.RotAngleXStatsTwist method) (cryocat.analysis.tango.RotAngleYStatsTwist method) (cryocat.analysis.tango.RotAngleZStatsTwist method) compute_alignment_statistics() (in module cryocat.analysis.sta) compute_alpha_complex() (cryocat.analysis.tango.AlphaComplexDescriptor method) compute_center_peak_stats_and_profiles() (in module cryocat.analysis.pana) compute_ctf_1d() (in module cryocat.core.cryomap) compute_diameter() (cryocat.analysis.structure.NPC static method) compute_dist_maps_voxels() (in module cryocat.analysis.pana) compute_features() (cryocat.analysis.tango.AlphaComplexDescriptor method) (cryocat.analysis.tango.PLComplexDescriptor method) compute_frequency_array() (in module cryocat.utils.mathutils) compute_gaussian_threshold() (in module cryocat.analysis.tmana) compute_intersection() (cryocat.analysis.structure.PleomorphicSurface static method) compute_kde() (cryocat.analysis.visplot.KDEBuilder method) compute_normals() (cryocat.analysis.structure.PleomorphicSurface static method) compute_otsu_threshold() (cryocat.core.cryomotl.Motl method) compute_outer_edges() (cryocat.analysis.tango.PLComplexDescriptor method) compute_pca() (cryocat.analysis.tango.Descriptor method) compute_peak_shapes() (in module cryocat.analysis.pana) compute_point_surface_distance() (cryocat.analysis.structure.PleomorphicSurface static method) compute_rmse() (in module cryocat.utils.mathutils) compute_scores_map_threshold_triangle() (in module cryocat.analysis.tmana) compute_sharp_mask_overlap() (in module cryocat.analysis.pana) compute_solidity() (in module cryocat.core.cryomask) compute_stats() (cryocat.analysis.tango.Feature method) compute_triangles() (cryocat.analysis.tango.PLComplexDescriptor method) Cone (class in cryocat.analysis.tango) cone_distance() (in module cryocat.utils.geom) cone_in_plane_decomp() (cryocat.utils.geom.Matrix method) cone_indicator() (cryocat.utils.geom.Point3D method) cone_inplane_distance() (in module cryocat.utils.geom) consume() (cryocat.utils.starfileio.Token static method) convert_angles_from_relion() (cryocat.core.cryomotl.RelionMotl method) convert_angles_to_relion() (cryocat.core.cryomotl.RelionMotl method) convert_color_scheme() (in module cryocat.analysis.visplot) convert_coordinates_ang_merge() (cryocat.core.cryomotl.RelionMotlv5 method) convert_coordinates_merge() (cryocat.core.cryomotl.RelionMotlv5 method) convert_section_type() (cryocat.core.mdoc.Mdoc method) convert_shifts() (cryocat.core.cryomotl.RelionMotl method) convert_to_dynamo_motl() (cryocat.core.cryomotl.DynamoMotl static method) convert_to_mod_motl() (cryocat.core.cryomotl.ModMotl static method) convert_to_motl() (cryocat.core.cryomotl.DynamoMotl method) (cryocat.core.cryomotl.EmMotl method) (cryocat.core.cryomotl.ModMotl method) (cryocat.core.cryomotl.Motl method) (cryocat.core.cryomotl.RelionMotl method) (cryocat.core.cryomotl.RelionMotlv5 method) (cryocat.core.cryomotl.StopgapMotl method) convert_to_particle_list() (in module cryocat.analysis.tango) convert_to_radial() (in module cryocat.analysis.visplot) convert_to_sg_motl() (cryocat.core.cryomotl.StopgapMotl static method) convert_to_spherical() (in module cryocat.analysis.visplot) correct_bbox() (in module cryocat.analysis.pana) correct_order() (cryocat.core.tiltstack.TiltStack method) CountSHOT (class in cryocat.analysis.tango) create_additional_descriptors() (cryocat.analysis.tango.CustomDescriptor method) create_angular_distance_maps() (in module cryocat.analysis.tmana) create_denovo_multiref_run() (in module cryocat.analysis.sta) create_em_path() (in module cryocat.analysis.pana) create_empty_motl_df() (cryocat.core.cryomotl.Motl static method) create_final_output() (cryocat.core.cryomotl.RelionMotl method) create_multiref_run() (in module cryocat.analysis.sta) create_optics_group_v3_1() (cryocat.core.cryomotl.RelionMotl method) create_optics_group_v4() (cryocat.core.cryomotl.RelionMotl method) create_optics_group_v5() (cryocat.core.cryomotl.RelionMotlv5 method) create_output_base_name() (in module cryocat.analysis.pana) create_output_folder_name() (in module cryocat.analysis.pana) create_output_folder_path() (in module cryocat.analysis.pana) create_particles_data() (cryocat.core.cryomotl.RelionMotl method) (cryocat.core.cryomotl.RelionMotlv5 method) create_projection() (in module cryocat.analysis.visplot) create_relion_df() (cryocat.core.cryomotl.RelionMotl method) (cryocat.core.cryomotl.RelionMotlv5 method) create_smooth_polar_histogram() (in module cryocat.analysis.visplot) create_spherical_oversampling() (cryocat.analysis.structure.PleomorphicSurface static method) create_starting_parameters_1D() (in module cryocat.analysis.tmana) create_starting_parameters_2D() (in module cryocat.analysis.tmana) create_structure_path() (in module cryocat.analysis.pana) create_subtomo_name() (in module cryocat.analysis.pana) create_subtomograms_for_tm() (in module cryocat.analysis.pana) create_summary_pdf() (in module cryocat.analysis.pana) create_tomo_name() (in module cryocat.analysis.pana) create_vertex_volume() (in module cryocat.analysis.memthick) create_wedge_list_em_batch() (in module cryocat.utils.wedgeutils) create_wedge_list_sg() (in module cryocat.utils.wedgeutils) create_wedge_list_sg_batch() (in module cryocat.utils.wedgeutils) create_wedge_names() (in module cryocat.analysis.pana) create_wg_mask() (in module cryocat.utils.wedgeutils) crop() (in module cryocat.core.cryomap) (in module cryocat.core.tiltstack) cryoCAT module cryocat.analysis.memthick module cryocat.analysis.nnana module cryocat.analysis.pana module cryocat.analysis.ribana module cryocat.analysis.sta module cryocat.analysis.structure module cryocat.analysis.tango module cryocat.analysis.tmana module cryocat.analysis.visplot module cryocat.core.cryomap module cryocat.core.cryomask module cryocat.core.cryomotl module cryocat.core.mdoc module cryocat.core.tiltstack module cryocat.utils.geom module cryocat.utils.ioutils module cryocat.utils.mathutils module cryocat.utils.starfileio module cryocat.utils.wedgeutils module ctffind4_read() (in module cryocat.utils.ioutils) cube() (in module cryocat.utils.geom) CustomDescriptor (class in cryocat.analysis.tango) CustomSupport (class in cryocat.analysis.tango) cut_the_best_subtomo() (in module cryocat.analysis.pana) Cylinder (class in cryocat.analysis.tango) cylindrical_mask() (in module cryocat.core.cryomask) cylindrical_mask_from_points() (in module cryocat.core.cryomask) D deconvolve() (in module cryocat.core.cryomap) (in module cryocat.core.tiltstack) default_version (cryocat.core.cryomotl.RelionMotl attribute) Defaults (class in cryocat.analysis.visplot) defocus_load() (in module cryocat.utils.ioutils) defocus_remove_file_entries() (in module cryocat.utils.ioutils) Descriptor (class in cryocat.analysis.tango) df_load() (in module cryocat.utils.ioutils) dict_load() (in module cryocat.utils.ioutils) dict_write() (in module cryocat.utils.ioutils) difference() (in module cryocat.core.cryomask) dimensions_load() (in module cryocat.utils.ioutils) distance() (cryocat.analysis.tango.Particle method) distance_array() (in module cryocat.utils.geom) DistProductStatsTwist (class in cryocat.analysis.tango) dodecahedron() (in module cryocat.utils.geom) dose_filter() (in module cryocat.core.tiltstack) dose_filter_single_image() (in module cryocat.core.tiltstack) drop_duplicates() (cryocat.core.cryomotl.Motl method) drop_symmetric_duplicates() (cryocat.analysis.nnana.NearestNeighbors method) dual_basis_se3() (cryocat.utils.geom.Matrix method) dual_basis_so3() (cryocat.utils.geom.Matrix method) DynamoMotl (class in cryocat.core.cryomotl) E ellipsoid_mask() (in module cryocat.core.cryomask) ellipsoid_shell_mask() (in module cryocat.core.cryomask) em2mrc() (in module cryocat.core.cryomap) EmMotl (class in cryocat.core.cryomotl) emmotl2mod() (in module cryocat.core.cryomotl) emmotl2relion() (in module cryocat.core.cryomotl) emmotl2stopgap() (in module cryocat.core.cryomotl) equalize_histogram() (in module cryocat.core.tiltstack) equip_symmetry() (cryocat.analysis.tango.SymmParticle class method) EuclideanDistNN (class in cryocat.analysis.tango) EuclideanDistStatsTwist (class in cryocat.analysis.tango) euler_angles_to_normals() (in module cryocat.utils.geom) EulerCharAlphaComplex (class in cryocat.analysis.tango) evaluate_alignment() (in module cryocat.analysis.sta) evaluate_classification() (in module cryocat.analysis.sta) evaluate_multirun_stability() (in module cryocat.analysis.sta) evaluate_scores_map() (in module cryocat.analysis.tmana) extra_layout (cryocat.analysis.visplot.Defaults attribute) extract_and_validate_surface() (in module cryocat.analysis.memthick) extract_defocus_data() (in module cryocat.utils.ioutils) extract_intensity_profile() (in module cryocat.analysis.memthick) extract_subvolume() (in module cryocat.core.cryomap) extract_surface_points() (in module cryocat.analysis.memthick) F Feature (class in cryocat.analysis.tango) FeatureCatalog (class in cryocat.analysis.tango) fileformat_replace_pattern() (in module cryocat.utils.ioutils) fill() (cryocat.core.cryomotl.Motl method) fill_ellipsoid() (in module cryocat.utils.geom) fill_hollow_mask() (in module cryocat.core.cryomask) fill_wedge() (in module cryocat.analysis.visplot) Filter (class in cryocat.analysis.tango) filter_dist_maps() (in module cryocat.analysis.tmana) filter_features() (cryocat.analysis.tango.Descriptor method) filter_intensity_profiles() (in module cryocat.analysis.memthick) filter_nn_radial_stats() (in module cryocat.analysis.nnana) FilterCatalog (class in cryocat.analysis.tango) find_all_possible_matches_kernel() (in module cryocat.analysis.memthick) find_matches_parallel() (in module cryocat.analysis.memthick) find_surface_neighbors() (in module cryocat.analysis.memthick) fit_circle_2d_lsq() (in module cryocat.utils.geom) fit_circle_2d_newton() (in module cryocat.utils.geom) fit_circle_3d_lsq() (in module cryocat.utils.geom) fit_circle_3d_pratt() (in module cryocat.utils.geom) fit_circle_3d_taubin() (in module cryocat.utils.geom) fit_ellipsoid() (in module cryocat.utils.geom) fix_relion5_star() (cryocat.utils.starfileio.Starfile static method) fixed_cone_directions() (cryocat.analysis.tango.SHOTDescriptor method) flip() (in module cryocat.core.cryomap) flip_along_axes() (in module cryocat.core.tiltstack) flip_handedness() (cryocat.core.cryomotl.Motl method) font_family (cryocat.analysis.visplot.Defaults attribute) font_size (cryocat.analysis.visplot.Defaults attribute) format_input_data() (in module cryocat.analysis.visplot) format_input_data_id() (in module cryocat.analysis.visplot) fsc_read() (in module cryocat.utils.ioutils) fsc_write() (in module cryocat.utils.ioutils) G gctf_read() (in module cryocat.utils.ioutils) generate_angles() (in module cryocat.utils.geom) generate_ctf() (in module cryocat.analysis.pana) generate_exposure() (in module cryocat.analysis.pana) generate_mask() (in module cryocat.core.cryomask) generate_matching_statistics() (in module cryocat.analysis.memthick) generate_rotated_axes() (cryocat.analysis.tango.SHOTDescriptor method) generate_thickness_volume() (in module cryocat.analysis.memthick) generate_wedge_masks() (in module cryocat.analysis.pana) generate_wedgemask_slices_template() (in module cryocat.analysis.pana) generate_wedgemask_slices_tile() (in module cryocat.analysis.pana) GeodesicDistNN (class in cryocat.analysis.tango) GeodesicnDistStatsTwist (class in cryocat.analysis.tango) get_all_classes() (cryocat.analysis.tango.Catalog method) get_all_feature_ids() (cryocat.analysis.tango.TwistDescriptor static method) get_all_files_matching_pattern() (in module cryocat.utils.ioutils) get_all_pairs() (in module cryocat.utils.mathutils) get_angles() (cryocat.core.cryomotl.Motl method) get_angular_distances() (cryocat.analysis.nnana.NearestNeighbors method) get_axis_feature_id() (cryocat.analysis.tango.TwistDescriptor static method) get_axis_from_rotation() (in module cryocat.utils.geom) get_barycentric_motl() (cryocat.core.cryomotl.Motl method) get_bounding_box() (in module cryocat.core.cryomask) get_center_and_radius() (cryocat.analysis.structure.NPC static method) get_center_with_radius() (cryocat.analysis.structure.NPC static method) get_centers_as_motl() (cryocat.analysis.structure.NPC static method) get_central_label() (in module cryocat.analysis.tmana) get_central_plane_labels() (in module cryocat.analysis.tmana) get_centre_from_mean_subunit_location() (cryocat.analysis.structure.MAK method) get_chain_distances() (in module cryocat.analysis.ribana) get_class_occupancy() (in module cryocat.analysis.sta) get_class_polysome_occupancies_mdp() (in module cryocat.analysis.ribana) get_class_polysome_occupancies_mp() (in module cryocat.analysis.ribana) get_colormap_color() (in module cryocat.analysis.tango) get_colors_from_palette() (in module cryocat.analysis.visplot) get_coordinates() (cryocat.core.cryomotl.Motl method) get_correct_format() (in module cryocat.core.cryomask) get_cross_slices() (in module cryocat.core.cryomap) get_data_from_warp_xml() (in module cryocat.utils.ioutils) get_data_range() (cryocat.analysis.tango.TwistDescriptor class method) get_ellipsoid_label() (in module cryocat.analysis.tmana) get_feature() (cryocat.core.cryomotl.Motl method) get_feature_nn() (in module cryocat.analysis.ribana) get_feature_nn_indices() (in module cryocat.analysis.nnana) (in module cryocat.analysis.ribana) get_feature_nn_within_radius() (in module cryocat.analysis.nnana) get_file_encoding() (in module cryocat.utils.ioutils) get_filename_from_path() (in module cryocat.utils.ioutils) get_files_prefix_suffix() (in module cryocat.utils.ioutils) get_filter_radius() (in module cryocat.core.cryomap) get_frame_and_comments() (cryocat.utils.starfileio.Starfile static method) get_image() (cryocat.core.mdoc.Mdoc method) get_image_by_zvalue() (cryocat.core.mdoc.Mdoc method) get_image_by_zvalue_range() (cryocat.core.mdoc.Mdoc method) get_image_feature() (cryocat.core.mdoc.Mdoc method) get_image_features() (cryocat.core.mdoc.Mdoc method) get_images() (cryocat.core.mdoc.Mdoc method) get_images_by_zvalue_ranges() (cryocat.core.mdoc.Mdoc method) get_images_by_zvalues() (cryocat.core.mdoc.Mdoc method) get_important_features() (cryocat.analysis.tango.Descriptor method) get_indices() (in module cryocat.analysis.pana) get_mask_stats() (in module cryocat.analysis.pana) get_mass_center() (in module cryocat.core.cryomask) get_mass_dimensions() (in module cryocat.core.cryomask) get_max_number_digits() (cryocat.core.cryomotl.Motl method) get_mixed_feature_ids() (cryocat.analysis.tango.TwistDescriptor static method) get_monosome_stats() (in module cryocat.analysis.ribana) get_motl_extension() (in module cryocat.analysis.sta) get_motl_filename() (in module cryocat.analysis.sta) get_motl_intersection() (cryocat.core.cryomotl.Motl class method) get_motl_subset() (cryocat.core.cryomotl.Motl method) get_neighbor_surface_points() (in module cryocat.analysis.memthick) get_new_subunit_idx() (cryocat.analysis.structure.NPC static method) get_nn_dist() (in module cryocat.analysis.ribana) get_nn_distances() (in module cryocat.analysis.nnana) (in module cryocat.analysis.ribana) get_nn_rotations() (cryocat.analysis.nnana.NearestNeighbors method) (in module cryocat.analysis.nnana) (in module cryocat.analysis.ribana) get_nn_stats() (in module cryocat.analysis.nnana) (in module cryocat.analysis.ribana) get_nn_stats_within_radius() (in module cryocat.analysis.nnana) get_nn_subset() (cryocat.analysis.nnana.NearestNeighbors method) get_nn_twist_stats_within_radius() (cryocat.analysis.tango.TwistDescriptor static method) get_nn_within_distance() (in module cryocat.analysis.nnana) get_nn_within_radius() (in module cryocat.analysis.nnana) get_normalized_coord() (cryocat.analysis.nnana.NearestNeighbors method) get_number_of_digits() (in module cryocat.utils.mathutils) get_number_of_lines_with_character() (in module cryocat.utils.ioutils) get_parametric_description() (cryocat.analysis.structure.PleomorphicSurface static method) get_polysome_stats() (in module cryocat.analysis.ribana) get_pos_feature_ids() (cryocat.analysis.tango.TwistDescriptor static method) get_qp_rotations() (cryocat.analysis.nnana.NearestNeighbors method) get_qp_twist_desc() (cryocat.analysis.tango.TwistDescriptor method) get_random_subset() (cryocat.core.cryomotl.Motl method) get_relative_position() (cryocat.core.cryomotl.Motl method) get_rot_feature_ids() (cryocat.analysis.tango.TwistDescriptor static method) get_rotations() (cryocat.core.cryomotl.Motl method) (in module cryocat.analysis.ribana) get_shape_stats() (in module cryocat.analysis.pana) get_sharp_mask_stats() (in module cryocat.analysis.pana) get_similar_size_factors() (in module cryocat.utils.mathutils) get_soft_mask_stats() (in module cryocat.analysis.pana) get_specifier_id() (cryocat.utils.starfileio.Starfile static method) get_stable_particles() (in module cryocat.analysis.sta) get_start_end_indices() (in module cryocat.core.cryomap) get_subtomos_class_stability() (in module cryocat.analysis.sta) get_symm_parameters() (cryocat.analysis.tango.TwistDescriptor static method) get_tilt_angles() (in module cryocat.core.mdoc) get_twist_mixed_df() (cryocat.analysis.tango.TwistDescriptor method) get_twist_mixed_np() (cryocat.analysis.tango.TwistDescriptor method) get_twist_pos_df() (cryocat.analysis.tango.TwistDescriptor method) get_twist_pos_np() (cryocat.analysis.tango.TwistDescriptor method) get_twist_rot_df() (cryocat.analysis.tango.TwistDescriptor method) get_twist_rot_np() (cryocat.analysis.tango.TwistDescriptor method) get_unique_values() (cryocat.analysis.nnana.NearestNeighbors method) (cryocat.core.cryomotl.Motl method) get_version_from_file() (cryocat.core.cryomotl.RelionMotl static method) get_version_specific_names() (cryocat.core.cryomotl.RelionMotl static method) great_circle_distance() (in module cryocat.utils.geom) great_circle_distance_matrix() (in module cryocat.utils.geom) H hausdorff_distance_sphere() (in module cryocat.utils.geom) height (cryocat.analysis.visplot.Defaults attribute) highpass() (in module cryocat.core.cryomap) Hist2DBuilder (class in cryocat.analysis.visplot) HistBuilder (class in cryocat.analysis.visplot) I icosahedron() (in module cryocat.utils.geom) identity() (cryocat.analysis.tango.Particle class method) imod_com_read() (in module cryocat.utils.ioutils) in_plane_angle() (cryocat.analysis.tango.Particle method) (cryocat.utils.geom.Matrix method) indices_load() (in module cryocat.utils.ioutils) indices_reset() (in module cryocat.utils.ioutils) inner_angles() (cryocat.utils.geom.Triangle method) inplane_distance() (in module cryocat.utils.geom) inscribed_circle() (cryocat.utils.geom.Triangle method) int_profiles_extract_clean() (in module cryocat.analysis.memthick) interpolate_between_points() (in module cryocat.analysis.memthick) interpolate_between_vertices() (in module cryocat.analysis.memthick) interpolate_surface_if_requested() (in module cryocat.analysis.memthick) interpolate_surface_points() (in module cryocat.analysis.memthick) intersection() (in module cryocat.core.cryomask) inv() (cryocat.analysis.tango.Particle method) invert_contrast() (in module cryocat.core.cryomap) is_float() (in module cryocat.utils.ioutils) is_SE3() (cryocat.utils.geom.Matrix method) is_SO3() (cryocat.utils.geom.Matrix method) is_surface_point() (in module cryocat.analysis.memthick) K k_means_clustering() (cryocat.analysis.tango.Descriptor method) KDEBuilder (class in cryocat.analysis.visplot) keep_image() (cryocat.core.mdoc.Mdoc method) keep_images() (cryocat.core.mdoc.Mdoc method) kept_images() (cryocat.core.mdoc.Mdoc method) L Line (class in cryocat.utils.geom) LineSegment (class in cryocat.utils.geom) LinkTypeAlphaComplex (class in cryocat.analysis.tango) list_max() (cryocat.analysis.visplot.KDEBuilder method) LITERAL (cryocat.utils.starfileio.TokenType attribute) load() (cryocat.analysis.tango.CustomDescriptor class method) (cryocat.analysis.tango.TwistDescriptor class method) (cryocat.core.cryomotl.Motl class method) load_parametric_surface() (cryocat.analysis.structure.PleomorphicSurface static method) load_wedge_list_em() (in module cryocat.utils.wedgeutils) load_wedge_list_sg() (in module cryocat.utils.wedgeutils) log() (cryocat.analysis.memthick.MeshNormalVoter method) lookahead() (cryocat.utils.starfileio.Token static method) LOOP (cryocat.utils.starfileio.TokenType attribute) lowpass() (in module cryocat.core.cryomap) M main() (in module cryocat.analysis.memthick) MAK (class in cryocat.analysis.structure) make_angles_canonical() (cryocat.core.cryomotl.Motl method) map_tight_mask() (in module cryocat.core.cryomask) margin (cryocat.analysis.visplot.Defaults attribute) mask_overlap() (in module cryocat.core.cryomask) Matrix (class in cryocat.utils.geom) matrix_power() (cryocat.utils.geom.Matrix method) max_dissimilarity() (cryocat.analysis.tango.SymmParticle method) Mdoc (class in cryocat.core.mdoc) measure_membrane_thickness() (in module cryocat.analysis.memthick) measure_thickness_cpu() (in module cryocat.analysis.memthick) measure_thickness_gpu() (in module cryocat.analysis.memthick) merge() (in module cryocat.core.tiltstack) merge_and_drop_duplicates() (cryocat.core.cryomotl.Motl class method) merge_and_renumber() (cryocat.core.cryomotl.Motl class method) merge_mdoc_files() (in module cryocat.core.mdoc) merge_rings() (cryocat.analysis.structure.NPC static method) merge_subunits() (cryocat.analysis.structure.NPC static method) MeshNormalVoter (class in cryocat.analysis.memthick) min_great_circle_distance() (in module cryocat.utils.geom) MixedDistNN (class in cryocat.analysis.tango) mod2emmotl() (in module cryocat.core.cryomotl) ModMotl (class in cryocat.core.cryomotl) module cryoCAT cryocat.analysis.memthick cryocat.analysis.nnana cryocat.analysis.pana cryocat.analysis.ribana cryocat.analysis.sta cryocat.analysis.structure cryocat.analysis.tango cryocat.analysis.tmana cryocat.analysis.visplot cryocat.core.cryomap cryocat.core.cryomask cryocat.core.cryomotl cryocat.core.mdoc cryocat.core.tiltstack cryocat.utils.geom cryocat.utils.ioutils cryocat.utils.mathutils cryocat.utils.starfileio cryocat.utils.wedgeutils molmap_tight_mask() (in module cryocat.core.cryomask) Motl (class in cryocat.core.cryomotl) motl_columns (cryocat.core.cryomotl.Motl attribute) mrc2em() (in module cryocat.core.cryomap) N n_gon_points() (in module cryocat.utils.geom) NearestNeighbors (class in cryocat.analysis.nnana) NEWLINE (cryocat.utils.starfileio.TokenType attribute) NNCountTwist (class in cryocat.analysis.tango) normalize() (in module cryocat.core.cryomap) normalize_ranges() (cryocat.analysis.visplot.KDEBuilder method) normalize_tomogram() (in module cryocat.analysis.memthick) normalize_under_mask() (in module cryocat.core.cryomap) normalize_vector() (in module cryocat.utils.geom) normalize_vectors() (in module cryocat.utils.geom) normals_to_euler_angles() (in module cryocat.utils.geom) NPC (class in cryocat.analysis.structure) number_of_cone_rotations() (in module cryocat.utils.geom) O octahedron() (in module cryocat.utils.geom) one_value_per_line_read() (in module cryocat.utils.ioutils) order_points_on_circle() (in module cryocat.utils.geom) orient_normals() (cryocat.analysis.memthick.MeshNormalVoter method) otsu_threshold() (in module cryocat.utils.mathutils) oversample_spline() (in module cryocat.utils.geom) P pad() (in module cryocat.core.cryomap) padded_limits() (cryocat.analysis.visplot.KDEBuilder method) pairs (cryocat.core.cryomotl.StopgapMotl attribute) parse_arguments() (in module cryocat.analysis.memthick) parse_column() (cryocat.utils.starfileio.Token static method) parse_columns() (cryocat.utils.starfileio.Token static method) parse_newline_or_comments() (cryocat.utils.starfileio.Token static method) parse_rows() (cryocat.utils.starfileio.Token static method) parse_shape_string() (in module cryocat.core.cryomask) parse_specifier() (cryocat.utils.starfileio.Token static method) parse_subtomo_id() (cryocat.core.cryomotl.RelionMotl method) parse_tomo_id() (cryocat.core.cryomotl.RelionMotl method) Particle (class in cryocat.analysis.tango) pca_analysis() (cryocat.analysis.tango.Descriptor method) pixels2resolution() (in module cryocat.core.cryomap) place_object() (in module cryocat.core.cryomap) PLComplexDescriptor (class in cryocat.analysis.tango) PleomorphicSurface (class in cryocat.analysis.structure) plot_alignment_stability() (in module cryocat.analysis.visplot) plot_class_occupancy() (in module cryocat.analysis.visplot) plot_class_stability() (in module cryocat.analysis.visplot) plot_classification_convergence() (in module cryocat.analysis.visplot) plot_fsc() (in module cryocat.analysis.visplot) plot_graph() (cryocat.analysis.visplot.BaseBuilder method) plot_histogram() (in module cryocat.analysis.visplot) plot_histogram2D() (in module cryocat.analysis.visplot) plot_k_means() (cryocat.analysis.tango.Descriptor method) plot_kde() (in module cryocat.analysis.visplot) plot_kernel_density_estimation() (in module cryocat.analysis.visplot) plot_line() (in module cryocat.analysis.visplot) plot_nn_coord() (in module cryocat.analysis.nnana) (in module cryocat.analysis.ribana) plot_nn_coord_df() (in module cryocat.analysis.nnana) (in module cryocat.analysis.ribana) plot_nn_rot_coord_df() (in module cryocat.analysis.nnana) (in module cryocat.analysis.ribana) plot_nn_rot_coord_df_plotly() (in module cryocat.analysis.nnana) plot_orientational_distribution() (in module cryocat.analysis.visplot) plot_pca_summary() (in module cryocat.analysis.visplot) plot_polar_nn_distances() (in module cryocat.analysis.visplot) plot_scatter2D() (in module cryocat.analysis.visplot) plot_scores_and_peaks() (in module cryocat.analysis.pana) plot_single() (cryocat.analysis.visplot.BaseBuilder method) (cryocat.analysis.visplot.Hist2DBuilder method) (cryocat.analysis.visplot.HistBuilder method) (cryocat.analysis.visplot.KDEBuilder method) (cryocat.analysis.visplot.ScatterBuilder method) plot_spherical_density() (in module cryocat.analysis.visplot) plot_spherical_density_hist2d() (in module cryocat.analysis.visplot) plot_subplots() (cryocat.analysis.visplot.BaseBuilder method) (cryocat.analysis.visplot.Hist2DBuilder method) (cryocat.analysis.visplot.HistBuilder method) (cryocat.analysis.visplot.KDEBuilder method) (cryocat.analysis.visplot.ScatterBuilder method) Point3D (class in cryocat.utils.geom) point_ellipsoid_distance() (in module cryocat.utils.geom) point_pairwise_dist() (in module cryocat.utils.geom) postprocess() (in module cryocat.core.cryomask) prepare_optics_data() (cryocat.core.cryomotl.RelionMotl method) (cryocat.core.cryomotl.RelionMotlv5 method) prepare_particles_data() (cryocat.core.cryomotl.RelionMotl method) (cryocat.core.cryomotl.RelionMotlv5 method) prepare_trace_kwargs() (cryocat.analysis.visplot.Hist2DBuilder method) preprocess_params() (in module cryocat.core.cryomask) print_summary() (in module cryocat.analysis.memthick) process() (cryocat.analysis.memthick.MeshNormalVoter method) process_matches_cpu2cpu() (in module cryocat.analysis.memthick) process_matches_gpu2cpu() (in module cryocat.analysis.memthick) process_membrane_segmentation() (in module cryocat.analysis.memthick) process_second_axis_data() (cryocat.analysis.visplot.BaseBuilder method) process_tomo_twist() (cryocat.analysis.tango.TwistDescriptor static method) project_3d_points_on_2d_plane_normal_aligned() (in module cryocat.utils.geom) project_3d_points_on_2d_plane_variance_based() (in module cryocat.utils.geom) project_equidistant() (in module cryocat.analysis.visplot) project_lambert() (in module cryocat.analysis.visplot) project_points_on_plane_with_preserved_distance() (in module cryocat.utils.geom) project_points_on_sphere() (in module cryocat.analysis.visplot) project_stereo() (in module cryocat.analysis.visplot) PROPERTY (cryocat.utils.starfileio.TokenType attribute) proximity_clustering() (cryocat.analysis.tango.Descriptor method) px_defaults() (in module cryocat.analysis.visplot) Q quaternion_log() (in module cryocat.utils.geom) quaternion_mult() (in module cryocat.utils.geom) R random() (cryocat.analysis.tango.Particle class method) randomize_phases() (in module cryocat.utils.mathutils) ray_ellipsoid_intersection_3d() (in module cryocat.utils.geom) ray_ray_intersection_3d() (in module cryocat.utils.geom) read() (cryocat.utils.starfileio.Starfile static method) (in module cryocat.core.cryomap) read_hdf5() (in module cryocat.core.cryomap) read_in() (cryocat.analysis.tango.TwistDescriptor static method) (cryocat.core.cryomotl.DynamoMotl static method) (cryocat.core.cryomotl.EmMotl static method) (cryocat.core.cryomotl.ModMotl static method) (cryocat.core.cryomotl.RelionMotl method) (cryocat.core.cryomotl.RelionMotlv5 method) (cryocat.core.cryomotl.StopgapMotl static method) read_in_tomograms() (cryocat.core.cryomotl.RelionMotlv5 method) read_segmentation() (in module cryocat.analysis.memthick) read_tomo() (in module cryocat.analysis.memthick) recenter() (in module cryocat.core.cryomap) recenter_to_subparticle() (cryocat.core.cryomotl.Motl static method) recompute_dist_maps() (in module cryocat.analysis.pana) refine_mesh_normals() (in module cryocat.analysis.memthick) refine_normals() (cryocat.analysis.memthick.MeshNormalVoter method) refine_normals_and_separate_surfaces() (in module cryocat.analysis.memthick) register_colorscale() (in module cryocat.analysis.visplot) register_palette() (in module cryocat.analysis.visplot) relion2emmotl() (in module cryocat.core.cryomotl) relion2stopgap() (in module cryocat.core.cryomotl) relion2warp() (cryocat.core.cryomotl.RelionMotlv5 method) relion_ctffind4_read() (in module cryocat.utils.ioutils) RelionMotl (class in cryocat.core.cryomotl) RelionMotlv5 (class in cryocat.core.cryomotl) RelionMotlv5_1 (class in cryocat.core.cryomotl) remove_feature() (cryocat.core.cryomotl.Motl method) remove_image() (cryocat.core.mdoc.Mdoc method) remove_images() (cryocat.core.mdoc.Mdoc method) (in module cryocat.core.mdoc) remove_lines() (cryocat.utils.starfileio.Starfile static method) (in module cryocat.utils.ioutils) remove_nans() (cryocat.analysis.tango.Descriptor static method) remove_out_of_bounds_particles() (cryocat.core.cryomotl.Motl method) remove_tilts() (in module cryocat.core.tiltstack) removed_images() (cryocat.core.mdoc.Mdoc method) rename_folders() (in module cryocat.analysis.pana) rename_scores_angles() (in module cryocat.analysis.pana) renumber_objects_sequentially() (cryocat.core.cryomotl.Motl method) renumber_particles() (cryocat.core.cryomotl.Motl method) reorder_images() (cryocat.core.mdoc.Mdoc method) reset_images() (cryocat.core.mdoc.Mdoc method) resolution2pixels() (in module cryocat.core.cryomap) resolve_colors_any() (in module cryocat.analysis.visplot) resolve_colorscale() (in module cryocat.analysis.visplot) resolve_palette() (in module cryocat.analysis.visplot) rot_angles_load() (in module cryocat.utils.ioutils) RotAngleXStatsTwist (class in cryocat.analysis.tango) RotAngleYStatsTwist (class in cryocat.analysis.tango) RotAngleZStatsTwist (class in cryocat.analysis.tango) rotate() (in module cryocat.core.cryomap) (in module cryocat.core.cryomask) rotate_image() (in module cryocat.analysis.pana) rotate_points_rodrigues() (in module cryocat.utils.geom) run_analysis() (in module cryocat.analysis.pana) run_angle_analysis() (in module cryocat.analysis.pana) run_full_pipeline() (in module cryocat.analysis.memthick) S sample_cone() (in module cryocat.utils.geom) save_int_results() (in module cryocat.analysis.memthick) save_matching_statistics() (in module cryocat.analysis.memthick) save_thickness_volume() (in module cryocat.analysis.memthick) save_vertices_mrc_helper() (in module cryocat.analysis.memthick) scale() (cryocat.analysis.tango.Particle method) (in module cryocat.core.cryomap) scale_coordinates() (cryocat.core.cryomotl.Motl method) scatter_with_histogram() (in module cryocat.analysis.visplot) ScatterBuilder (class in cryocat.analysis.visplot) scores_extract_particles() (in module cryocat.analysis.tmana) SE3_cleanup() (cryocat.utils.geom.Matrix method) select_peaks() (in module cryocat.analysis.tmana) separate_bilayer() (cryocat.analysis.memthick.MeshNormalVoter method) set_axis_and_columns() (cryocat.analysis.tango.Support static method) set_defaults() (in module cryocat.analysis.visplot) set_pixel_size() (cryocat.core.cryomotl.RelionMotl method) set_version() (cryocat.core.cryomotl.RelionMotl method) set_version_specific_names() (cryocat.core.cryomotl.RelionMotl method) setup_logger() (in module cryocat.analysis.memthick) sg_df_reset_index() (cryocat.core.cryomotl.StopgapMotl static method) Shell (class in cryocat.analysis.tango) shift() (in module cryocat.core.cryomap) shift2() (in module cryocat.core.cryomap) shift_positions() (cryocat.core.cryomotl.Motl method) SHOTDescriptor (class in cryocat.analysis.tango) showlegend (cryocat.analysis.visplot.Defaults attribute) shrink_full_mask() (in module cryocat.core.cryomask) similarity_symm() (cryocat.analysis.tango.SymmParticle method) sort_by_distance() (cryocat.analysis.tango.TwistDescriptor method) sort_by_tilt() (cryocat.core.mdoc.Mdoc method) sort_files_by_idx() (in module cryocat.utils.ioutils) sort_mdoc_by_tilt_angles() (in module cryocat.core.mdoc) sort_tilts_by_angle() (in module cryocat.core.tiltstack) special_euclidean_from_rot_translation() (cryocat.utils.geom.Matrix method) Sphere (class in cryocat.analysis.tango) spherical_mask() (in module cryocat.core.cryomask) spherical_shell_mask() (in module cryocat.core.cryomask) spline_sampling() (in module cryocat.utils.geom) split_by_feature() (cryocat.core.cryomotl.Motl method) split_in_asymmetric_subunits() (cryocat.core.cryomotl.Motl method) split_mdoc_file() (in module cryocat.core.mdoc) split_stack_even_odd() (in module cryocat.core.tiltstack) Starfile (class in cryocat.utils.starfileio) stopgap2emmotl() (in module cryocat.core.cryomotl) stopgap2relion() (in module cryocat.core.cryomotl) StopgapMotl (class in cryocat.core.cryomotl) subtraction() (in module cryocat.core.cryomask) Support (class in cryocat.analysis.tango) SupportCatalog (class in cryocat.analysis.tango) symmetrize_volume() (in module cryocat.core.cryomap) symmetry_statistics() (cryocat.analysis.tango.TwistDescriptor method) SymmParticle (class in cryocat.analysis.tango) T tangent_at_identity() (cryocat.analysis.tango.Particle method) tangent_subspace_projection() (cryocat.analysis.tango.Particle method) template (cryocat.analysis.visplot.Defaults attribute) tetrahedron() (in module cryocat.utils.geom) TiltStack (class in cryocat.core.tiltstack) tlt_load() (in module cryocat.utils.ioutils) to_layout_kwargs() (cryocat.analysis.visplot.Defaults method) Token (class in cryocat.utils.starfileio) tokenize() (cryocat.utils.starfileio.Token static method) TokenType (class in cryocat.utils.starfileio) tomogram_shell_mask() (in module cryocat.core.cryomask) Torus (class in cryocat.analysis.tango) torus_indicator() (cryocat.utils.geom.Point3D method) torus_section_indicator() (cryocat.utils.geom.Point3D method) total_dose_load() (in module cryocat.utils.ioutils) trace_chains() (in module cryocat.analysis.ribana) Triangle (class in cryocat.utils.geom) trim() (in module cryocat.core.cryomap) twist_from_skew_translation() (cryocat.utils.geom.Matrix method) twist_template_comparison() (cryocat.analysis.tango.TwistDescriptor method) twist_vector() (cryocat.analysis.tango.Particle method) TwistDescriptor (class in cryocat.analysis.tango) U unify_nn_orientations() (cryocat.analysis.structure.NPC static method) union() (in module cryocat.core.cryomask) update_coordinates() (cryocat.core.cryomotl.Motl method) update_graph_layout() (cryocat.analysis.visplot.BaseBuilder method) update_layout_settings() (cryocat.analysis.visplot.BaseBuilder method) update_mdoc_features() (in module cryocat.core.mdoc) update_pixel_size() (cryocat.core.mdoc.Mdoc method) update_vertex_volume_after_interpolation() (in module cryocat.analysis.memthick) use_defaults() (in module cryocat.analysis.visplot) V validate_seg_tomo_compatibility() (in module cryocat.analysis.memthick) vector_angular_distance() (in module cryocat.utils.geom) vector_angular_distance_signed() (in module cryocat.utils.geom) verify_and_save_outputs() (in module cryocat.analysis.memthick) visualize_angles() (in module cryocat.utils.geom) visualize_rotations() (in module cryocat.utils.geom) W warp2relion() (cryocat.core.cryomotl.RelionMotlv5 method) warp_ctf_read() (in module cryocat.utils.ioutils) wedge_list_sg_to_em() (in module cryocat.utils.wedgeutils) weighted_stats() (cryocat.analysis.tango.TwistDescriptor method) width (cryocat.analysis.visplot.Defaults attribute) write() (cryocat.core.mdoc.Mdoc method) (cryocat.utils.starfileio.Starfile static method) (in module cryocat.core.cryomap) write_hdf5() (in module cryocat.core.cryomap) write_out() (cryocat.analysis.tango.TwistDescriptor method) (cryocat.core.cryomotl.DynamoMotl method) (cryocat.core.cryomotl.EmMotl method) (cryocat.core.cryomotl.ModMotl method) (cryocat.core.cryomotl.Motl method) (cryocat.core.cryomotl.RelionMotl method) (cryocat.core.cryomotl.RelionMotlv5 method) (cryocat.core.cryomotl.StopgapMotl method) (cryocat.core.tiltstack.TiltStack method) (in module cryocat.core.cryomask) write_out_motl() (in module cryocat.analysis.sta) write_to_model_file() (cryocat.core.cryomotl.Motl method) X x (cryocat.utils.geom.Point3D property) Y y (cryocat.utils.geom.Point3D property) Z z (cryocat.utils.geom.Point3D property) z_shift_load() (in module cryocat.utils.ioutils)