Index A | B | C | D | E | F | G | H | I | J | 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_component() (cryocat.analysis.assembly.CnComplex method) add_field() (cryocat.core.mdoc.Mdoc method) add_gaussian() (in module cryocat.core.cryomask) add_motl_columns() (cryocat.analysis.nnana.NearestNeighbors method) add_noise() (cryocat.analysis.tango.Particle method) add_noise_and_project_to_so3() (cryocat.utils.geom.Matrix method) add_parent() (cryocat.analysis.assembly.CnComplex method) add_subunit_state() (cryocat.analysis.assembly.CnComplex method) add_traced_info() (cryocat.analysis.assembly.Chain method) add_xyz_heatmap_row() (in module cryocat.analysis.visplot) adopt_recovered() (cryocat.analysis.assembly.PleomorphicSurface method) agreement_histogram() (cryocat.analysis.sta.CoassignmentFactor method) align_points_to_xy_plane() (in module cryocat.utils.geom) align_z_axes() (in module cryocat.utils.geom) alpha (cryocat.utils.imod.ModelHeader attribute) alpha_shape_tetra() (cryocat.core.surface.Mesh static method) AlphaComplexDescriptor (class in cryocat.analysis.tango) analyse_intensity_profiles() (in module cryocat.analysis.memthick) AnalyticSurface (class in cryocat.core.surface) analyze_rotations() (in module cryocat.analysis.pana) angle_between_n_vectors() (in module cryocat.utils.geom) angle_between_vectors() (in module cryocat.utils.geom) angles_save() (in module cryocat.utils.ioutils) angular_dissimilarity() (cryocat.analysis.assembly.PolyhedralComplex method) (cryocat.utils.geom.Polyhedron method) angular_distance() (in module cryocat.utils.geom) angular_distances() (in module cryocat.analysis.nnana) angular_score() (in module cryocat.utils.symmetry) angular_score_for_c_symmetry() (in module cryocat.utils.geom) AngularScoreNN (class in cryocat.analysis.tango) AngularScoreStatsTwist (class in cryocat.analysis.tango) annotate_with_envelope() (cryocat.analysis.assembly.PleomorphicSurface method) apply_bandpass() (in module cryocat.utils.imageutils) apply_defaults() (in module cryocat.analysis.visplot) apply_fft_filter() (in module cryocat.utils.imageutils) apply_highpass() (in module cryocat.utils.imageutils) apply_lowpass() (in module cryocat.utils.imageutils) apply_normals_mask() (cryocat.core.surface.DiscreteSurface method) apply_one_hit_per_target_distance() (cryocat.core.surface.DiscreteSurface static method) apply_rotation() (cryocat.core.cryomotl.Motl method) apply_starting_and_offset() (in module cryocat.utils.geom) apply_tomo_rotation() (cryocat.core.cryomotl.Motl method) apply_vertex_mask() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) apply_volume_mask() (cryocat.core.surface.DiscreteSurface method) apply_wedge_mask() (in module cryocat.core.cryowedge) apply_wiener_radial() (in module cryocat.utils.imageutils) area() (cryocat.utils.geom.Triangle method) area_triangle() (in module cryocat.utils.geom) as_list() (in module cryocat.utils.classutils) as_motl() (cryocat.core.surface.OrientedPointCloud method) as_rotation() (in module cryocat.utils.geom) as_symmetry() (in module cryocat.utils.geom) as_triplet() (in module cryocat.utils.geom) assess_mesh() (cryocat.core.surface.Mesh method) assign_affiliation_distance_based() (cryocat.analysis.assembly.ParametricSurface method) assign_affiliation_intersection_based() (cryocat.analysis.assembly.ParametricSurface method) assign_affiliation_mask_based() (cryocat.analysis.assembly.ParametricSurface static method) assign_cc_extra_columns() (cryocat.core.cryomotl.RelionMotl method) assign_class_by_nn() (in module cryocat.analysis.nnana) 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_segmentation_metadata() (cryocat.core.surface.Mesh method) assign_shell_and_cone_ids() (cryocat.analysis.tango.SHOTDescriptor method) assign_subunit_order() (cryocat.analysis.assembly.CnComplex method) (cryocat.analysis.assembly.DnComplex method) (cryocat.analysis.assembly.NPC method) (cryocat.analysis.assembly.PolyhedralComplex method) (cryocat.analysis.assembly.SymmetricComplex method) attach_fsc() (cryocat.analysis.sta.StaParameters method) attach_log() (cryocat.analysis.sta.StaParameters method) axes() (cryocat.utils.symmetry.SymmGroup method) axis (cryocat.utils.imod.ObjectHeader attribute) AxisRot (class in cryocat.analysis.tango) B bandpass() (in module cryocat.core.cryomap) barycenter() (in module cryocat.utils.geom) base_params (cryocat.analysis.sta.StaRun attribute) BaseBuilder (class in cryocat.analysis.visplot) beta (cryocat.utils.imod.ModelHeader attribute) bin() (in module cryocat.core.tiltstack) binarize() (in module cryocat.core.cryomap) (in module cryocat.utils.imageutils) blacklevel (cryocat.utils.imod.ModelHeader attribute) Block (class in cryocat.analysis.sta) block_pixel_size (cryocat.analysis.assembly.PleomorphicSurface property) BlockDefinition (class in cryocat.analysis.assembly) BlockLayer (class in cryocat.analysis.assembly) blue (cryocat.utils.imod.ObjectHeader attribute) browse() (in module cryocat.analysis.visplot) browse_objects() (cryocat.analysis.assembly.PleomorphicSurface method) build_coassignment_factor() (in module cryocat.analysis.sta) build_ctx() (in module cryocat.analysis.sta) 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_params_record() (in module cryocat.analysis.pana) 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) BUILDER (cryocat.utils.classutils.GuiCategory attribute) C calculate_conjugates() (in module cryocat.utils.imageutils) calculate_flcf() (in module cryocat.utils.imageutils) calculate_masked_fsc() (in module cryocat.core.cryomap) calculate_total_dose_batch() (in module cryocat.core.tiltstack) canonical (cryocat.analysis.sta.StaParamSpec attribute) cartesian_to_spherical() (in module cryocat.utils.geom) cast_rays() (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) Catalog (class in cryocat.analysis.tango) category (cryocat.utils.classutils.GuiEntry attribute) center (cryocat.analysis.assembly.PolyhedralComplex attribute) centered_nn_coords() (in module cryocat.analysis.nnana) central_angle (cryocat.analysis.assembly.CnComplex property) central_angles() (cryocat.analysis.assembly.CnComplex method) (cryocat.analysis.assembly.NPC method) CentralAngleStatsAlphaComplex (class in cryocat.analysis.tango) CentralAngleStatsPLComplex (class in cryocat.analysis.tango) Chain (class in cryocat.analysis.assembly) change_frame_path() (cryocat.core.mdoc.Mdoc method) change_to_separate_graphs() (cryocat.analysis.visplot.BaseBuilder method) check() (cryocat.utils.starfileio.Token static method) check_data_consistency() (in module cryocat.core.cryowedge) 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_for_duplicates() (cryocat.analysis.assembly.CnComplex method) check_isWarp() (cryocat.core.cryomotl.RelionMotlv5 method) check_nn_columns() (cryocat.analysis.nnana.NearestNeighbors static method) check_object_grouping() (cryocat.analysis.assembly.PleomorphicSurface method) check_same_tiltseries() (in module cryocat.utils.ioutils) check_sequence() (cryocat.utils.imod.ImodHeader static method) check_then_consume() (cryocat.utils.starfileio.Token static method) check_twist_columns() (cryocat.analysis.tango.TwistDescriptor static method) circumcircle() (cryocat.utils.geom.Triangle method) circumcircle_radius() (cryocat.utils.geom.Triangle method) circumference() (cryocat.analysis.assembly.CnComplex method) (cryocat.analysis.assembly.NPC method) classify_pores() (cryocat.analysis.assembly.NPC method) clean_by_angle() (cryocat.analysis.assembly.PleomorphicSurface method) clean_by_directional_distance() (cryocat.core.cryomotl.Motl method) clean_by_distance() (cryocat.core.cryomotl.Motl method) clean_by_distance_to_points() (cryocat.core.cryomotl.Motl method) clean_by_mask_overlap() (cryocat.core.cryomotl.Motl method) clean_by_normals() (cryocat.analysis.assembly.ParametricSurface method) (cryocat.analysis.assembly.PleomorphicSurface method) clean_by_otsu() (cryocat.core.cryomotl.Motl method) clean_by_radius() (cryocat.analysis.assembly.ParametricSurface method) clean_by_tomo_mask() (cryocat.core.cryomotl.Motl method) clean_per_object() (cryocat.analysis.assembly.NPC method) (cryocat.analysis.assembly.SymmetricComplex method) clean_subtomo_name_column() (cryocat.core.cryomotl.RelionMotlv5 static method) clean_tomo_name_column() (cryocat.core.cryomotl.RelionMotlv5 static method) cleanup_mesh() (cryocat.core.surface.Mesh method) closest_symmetric_copy() (in module cryocat.utils.symmetry) cluster_subunits_to_rings() (cryocat.analysis.assembly.NPC static method) cmm_read() (in module cryocat.utils.ioutils) cn_site_vectors() (in module cryocat.utils.geom) CnComplex (class in cryocat.analysis.assembly) CoassignmentFactor (class in cryocat.analysis.sta) colorscale (cryocat.analysis.visplot.Defaults attribute) colorway (cryocat.analysis.visplot.Defaults attribute) columns (cryocat.core.cryomotl.ModMotl attribute) (cryocat.core.cryomotl.StopgapMotl attribute) (cryocat.core.surface.Ellipsoid 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) complete_from_source() (cryocat.core.cryomotl.RelionMotl method) complex_centers() (in module cryocat.analysis.assembly) compose_subtomo_mode() (in module cryocat.analysis.sta) 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_alignment_statistics_from_params() (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_conjugation_matrix() (in module cryocat.utils.symmetry) compute_ctf_1d() (in module cryocat.utils.imageutils) compute_ctf_2d() (in module cryocat.utils.imageutils) compute_curvatures() (cryocat.core.surface.Mesh method) compute_diameter() (cryocat.analysis.assembly.NPC static method) compute_dist_maps_voxels() (in module cryocat.analysis.pana) compute_distance_map() (in module cryocat.analysis.pana) compute_features() (cryocat.analysis.tango.AlphaComplexDescriptor method) (cryocat.analysis.tango.PLComplexDescriptor method) compute_frequency_array() (in module cryocat.utils.imageutils) compute_gaussian_threshold() (in module cryocat.analysis.tmana) compute_intersection() (cryocat.analysis.assembly.ParametricSurface method) compute_kde() (cryocat.analysis.visplot.KDEBuilder method) compute_mesh_properties() (cryocat.core.surface.Mesh method) compute_nearest_neighbor_distances() (cryocat.core.surface.OrientedPointCloud method) compute_normals() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.DiscreteSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) compute_normals_angle() (cryocat.analysis.assembly.ParametricSurface method) compute_otsu_threshold() (cryocat.core.cryomotl.Motl method) compute_outer_edges() (cryocat.analysis.tango.PLComplexDescriptor method) compute_pca() (cryocat.analysis.tango.Descriptor method) (in module cryocat.analysis.clustering) compute_peak_shapes() (in module cryocat.analysis.pana) compute_peak_stats() (in module cryocat.analysis.pana) compute_point_surface_distance() (cryocat.analysis.assembly.ParametricSurface method) compute_props() (cryocat.core.surface.Ellipsoid method) compute_relative_orientations() (in module cryocat.utils.geom) compute_rmse() (in module cryocat.utils.mathutils) compute_scores_map_threshold_triangle() (in module cryocat.analysis.tmana) compute_shape_stats_single() (in module cryocat.analysis.pana) compute_sharp_mask_overlap() (in module cryocat.analysis.pana) compute_sharp_mask_overlap_single() (in module cryocat.analysis.pana) compute_solidity() (in module cryocat.core.cryomask) compute_startidx_sequence() (in module cryocat.analysis.sta) compute_stats() (cryocat.analysis.tango.Feature method) compute_triangles() (cryocat.analysis.tango.PLComplexDescriptor method) compute_wiener_1d() (in module cryocat.utils.imageutils) 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) connect() (cryocat.analysis.assembly.PleomorphicSurface method) connected_component_clusters() (in module cryocat.analysis.clustering) consensus_groups() (in module cryocat.analysis.sta) consensus_motl() (in module cryocat.analysis.sta) ConsensusResult (class in cryocat.analysis.sta) consistency_groups() (cryocat.analysis.sta.CoassignmentFactor method) construct_rays() (in module cryocat.utils.geom) consume() (cryocat.utils.starfileio.Token static method) ContactSite (class in cryocat.analysis.assembly) continue_run_prefill() (in module cryocat.analysis.sta) contour (cryocat.utils.imod.ModelHeader attribute) ContourHeader (class in cryocat.utils.imod) contsize (cryocat.utils.imod.ObjectHeader attribute) convert_angles_from_relion() (cryocat.core.cryomotl.RelionMotl method) convert_angles_to_relion() (cryocat.core.cryomotl.RelionMotl method) 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_sg_motl() (cryocat.core.cryomotl.StopgapMotl static method) convex_hull() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) 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_affiliation() (cryocat.analysis.assembly.NPC method) (cryocat.analysis.assembly.SymmetricComplex 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.utils.geom) create_ref (cryocat.analysis.sta.StaParamContext attribute) create_relion_df() (cryocat.core.cryomotl.RelionMotl method) (cryocat.core.cryomotl.RelionMotlv5 method) create_run_folder() (in module cryocat.analysis.sta) create_spherical_oversampling() (cryocat.analysis.assembly.ParametricSurface 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_html() (in module cryocat.analysis.pana) create_summary_html_from_folder() (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.core.cryowedge) create_wedge_list_sg() (in module cryocat.core.cryowedge) create_wedge_list_sg_batch() (in module cryocat.core.cryowedge) create_wedge_names() (in module cryocat.analysis.pana) create_wg_mask() (in module cryocat.core.cryowedge) crop() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.DiscreteSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) (in module cryocat.core.cryomap) (in module cryocat.core.tiltstack) cryoCAT module cryocat.analysis.assembly module cryocat.analysis.clustering module cryocat.analysis.memthick module cryocat.analysis.nnana module cryocat.analysis.pana module cryocat.analysis.sta 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.cryowedge module cryocat.core.mdoc module cryocat.core.surface module cryocat.core.tiltstack module cryocat.utils.classutils module cryocat.utils.exceptions module cryocat.utils.geom module cryocat.utils.imageutils module cryocat.utils.imod module cryocat.utils.ioutils module cryocat.utils.mathutils module cryocat.utils.scriptutils module cryocat.utils.starfileio module cryocat.utils.symmetry module csum (cryocat.utils.imod.ModelHeader attribute) ctffind4_read() (in module cryocat.utils.ioutils) Cube (class in cryocat.utils.geom) CubicGrid (class in cryocat.utils.ioutils) CustomDescriptor (class in cryocat.analysis.tango) CustomSupport (class in cryocat.analysis.tango) cut_the_best_subtomo() (in module cryocat.analysis.pana) cyclic() (cryocat.analysis.assembly.BlockDefinition class method) CyclicGroup (class in cryocat.utils.symmetry) Cylinder (class in cryocat.analysis.tango) (class in cryocat.core.surface) cylindrical_mask() (in module cryocat.core.cryomask) cylindrical_mask_from_points() (in module cryocat.core.cryomask) D dbscan_cluster() (in module cryocat.analysis.clustering) dbscan_clustering() (cryocat.analysis.tango.Descriptor method) deconvolve() (in module cryocat.core.cryomap) (in module cryocat.core.tiltstack) default (cryocat.analysis.sta.StaParamSpec attribute) default_feature_columns() (cryocat.analysis.nnana.NearestNeighbors static method) (cryocat.analysis.tango.CustomDescriptor static method) (cryocat.analysis.tango.TwistDescriptor static method) (cryocat.core.cryomotl.Motl static method) 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) denovo_template_blocks() (in module cryocat.analysis.sta) derive_initial_state() (cryocat.analysis.assembly.CnComplex method) derive_nn_radius() (cryocat.analysis.tango.TwistDescriptor static method) Descriptor (class in cryocat.analysis.tango) detect() (cryocat.analysis.memthick.IntensityProfileAnalyzer method) df_load() (in module cryocat.utils.ioutils) diameter() (cryocat.analysis.assembly.CnComplex method) dict_load() (in module cryocat.utils.ioutils) dict_write() (in module cryocat.utils.ioutils) difference() (in module cryocat.core.cryomask) DihedralGroup (class in cryocat.utils.symmetry) dimensions_load() (in module cryocat.utils.ioutils) discrete_colorscale() (in module cryocat.analysis.visplot) DiscreteSurface (class in cryocat.core.surface) discretize_thickness_per_voxel() (in module cryocat.analysis.memthick) dist_map_stats() (in module cryocat.analysis.pana) distance() (cryocat.analysis.tango.Particle method) distance_array() (in module cryocat.utils.geom) distance_point_center() (cryocat.core.surface.AnalyticSurface method) (cryocat.core.surface.Cylinder method) (cryocat.core.surface.QuadricsM method) distance_point_surface() (cryocat.core.surface.AnalyticSurface method) (cryocat.core.surface.Cylinder method) (cryocat.core.surface.Ellipsoid method) (cryocat.core.surface.QuadricsM method) distance_to_pointcloud() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) distance_to_points() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) DistProductStatsTwist (class in cryocat.analysis.tango) DnComplex (class in cryocat.analysis.assembly) Dodecahedron (class in cryocat.utils.geom) dose_attenuator() (in module cryocat.utils.imageutils) dose_filter() (in module cryocat.core.tiltstack) dose_filter_single_image() (in module cryocat.core.tiltstack) downsample_pixel() (cryocat.core.surface.OrientedPointCloud method) drawmode (cryocat.utils.imod.ModelHeader attribute) (cryocat.utils.imod.ObjectHeader attribute) drop_duplicates() (cryocat.core.cryomotl.Motl method) drop_nans() (in module cryocat.analysis.clustering) drop_symmetric_duplicates() (cryocat.analysis.nnana.NearestNeighbors method) dtype (cryocat.analysis.sta.StaParamSpec attribute) dual_basis_se3() (cryocat.utils.geom.Matrix method) dual_basis_so3() (cryocat.utils.geom.Matrix method) DynamoMotl (class in cryocat.core.cryomotl) E effective_n_sites (cryocat.analysis.assembly.BlockDefinition property) Ellipsoid (class in cryocat.core.surface) 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) encoding (cryocat.utils.imod.ImodHeader attribute) end_iteration (cryocat.analysis.sta.StaParameters property) envelope_from_blocks() (cryocat.analysis.assembly.PleomorphicSurface method) envelope_from_faces() (cryocat.analysis.assembly.PleomorphicSurface method) envelopes (cryocat.analysis.assembly.PleomorphicSurface property) equalize_histogram() (in module cryocat.core.tiltstack) equalize_histogram_2d() (in module cryocat.utils.imageutils) equip_symmetry() (cryocat.analysis.tango.SymmParticle static method) EuclideanDistNN (class in cryocat.analysis.tango) EuclideanDistStatsTwist (class in cryocat.analysis.tango) euler_angles_load() (in module cryocat.utils.ioutils) euler_angles_to_normals() (in module cryocat.utils.geom) EulerCharAlphaComplex (class in cryocat.analysis.tango) evaluate_alignment() (in module cryocat.analysis.sta) evaluate_alignment_from_params() (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) existing_refs_template_blocks() (in module cryocat.analysis.sta) expand() (cryocat.analysis.assembly.PolyhedralComplex method) expand_motl() (in module cryocat.analysis.assembly) expand_motl_name() (in module cryocat.analysis.sta) extensions (cryocat.utils.classutils.GuiEntry attribute) extra_data (cryocat.utils.imod.ObjectHeader attribute) extra_layout (cryocat.analysis.visplot.Defaults attribute) extract_best_subtomogram() (in module cryocat.analysis.pana) extract_defocus_data() (in module cryocat.utils.ioutils) extract_midplane() (cryocat.core.surface.OrientedPointCloud method) extract_orthogonal_lines_1d() (in module cryocat.utils.imageutils) extract_orthogonal_slices_2d() (in module cryocat.utils.imageutils) extract_peak_orientations() (in module cryocat.analysis.tmana) extract_points() (cryocat.core.surface.OrientedPointCloud method) extract_region() (cryocat.analysis.assembly.PleomorphicSurface method) extract_submesh() (cryocat.core.surface.Mesh method) extract_subvolume() (in module cryocat.core.cryomap) F faces (cryocat.analysis.assembly.PleomorphicSurface property) Feature (class in cryocat.analysis.tango) feature_vectors() (cryocat.analysis.assembly.PolyhedralComplex method) 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) Filter (class in cryocat.analysis.tango) filter_by_number_nn() (cryocat.core.surface.OrientedPointCloud method) filter_dist_maps() (in module cryocat.analysis.tmana) filter_feature_columns() (in module cryocat.analysis.clustering) filter_features() (cryocat.analysis.tango.Descriptor method) filter_nn_radial_stats() (in module cryocat.analysis.nnana) filter_strings() (in module cryocat.utils.classutils) filter_template_df() (in module cryocat.analysis.pana) filter_triangles() (cryocat.core.surface.Mesh method) FilterCatalog (class in cryocat.analysis.tango) find_all_possible_matches_kernel() (in module cryocat.analysis.memthick) find_closest_quadric() (cryocat.core.surface.QuadricsM method) find_matching_overlap_row() (in module cryocat.analysis.pana) find_nn_indices() (in module cryocat.analysis.nnana) find_nn_within_radius() (in module cryocat.analysis.nnana) find_nn_within_self() (in module cryocat.analysis.nnana) find_peak_3d() (in module cryocat.utils.imageutils) 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) fit_geometry() (cryocat.analysis.assembly.PolyhedralComplex method) fit_to_points() (cryocat.core.surface.AnalyticSurface class method) (cryocat.core.surface.Cylinder class method) (cryocat.core.surface.Ellipsoid class method) fit_to_points_spline() (cryocat.core.surface.Cylinder class method) fix_relion5_star() (cryocat.utils.starfileio.Starfile static method) fixed_cone_directions() (cryocat.analysis.tango.SHOTDescriptor method) flagged_pores() (cryocat.analysis.assembly.NPC method) flags (cryocat.utils.imod.ContourHeader attribute) (cryocat.utils.imod.ModelHeader attribute) (cryocat.utils.imod.ObjectHeader attribute) flip() (in module cryocat.core.cryomap) flip_along_axes() (in module cryocat.core.tiltstack) flip_array() (in module cryocat.utils.imageutils) flip_handedness() (cryocat.core.cryomotl.Motl method) flip_normals() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.DiscreteSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) flip_site (cryocat.analysis.assembly.BlockDefinition attribute) fn (cryocat.utils.classutils.GuiEntry attribute) folder_name (cryocat.analysis.sta.StaRun attribute) font_family (cryocat.analysis.visplot.Defaults attribute) font_size (cryocat.analysis.visplot.Defaults attribute) frame_rotation() (in module cryocat.utils.geom) from_alpha_shape() (cryocat.core.surface.Mesh class method) from_array_like() (cryocat.core.surface.Ellipsoid class method) from_ball_pivoting() (cryocat.core.surface.Mesh class method) from_blocks() (cryocat.analysis.assembly.PleomorphicSurface class method) from_bytes() (cryocat.utils.imod.ContourHeader class method) (cryocat.utils.imod.ModelHeader class method) (cryocat.utils.imod.ObjectHeader class method) from_csv() (cryocat.analysis.assembly.ParametricSurface class method) from_df() (cryocat.core.surface.Ellipsoid class method) from_dict() (cryocat.analysis.sta.StaParameters class method) (cryocat.core.surface.Ellipsoid class method) from_file() (cryocat.analysis.sta.NovaStaParams class method) (cryocat.analysis.sta.StopgapParams class method) from_format (cryocat.analysis.sta.StaParamSpec attribute) from_mesh() (cryocat.core.surface.OrientedPointCloud class method) from_motl() (cryocat.analysis.assembly.Chain class method) (cryocat.analysis.assembly.ParametricSurface class method) (cryocat.core.surface.OrientedPointCloud class method) from_motl_filaments() (cryocat.core.surface.Mesh class method) from_motls() (cryocat.analysis.assembly.Chain class method) from_mrc() (cryocat.core.surface.Mesh class method) (cryocat.core.surface.OrientedPointCloud class method) from_open3d() (cryocat.core.surface.Mesh class method) from_ordered_path() (cryocat.core.surface.Mesh class method) from_parent() (cryocat.analysis.assembly.CnComplex class method) from_polyhedron() (cryocat.utils.symmetry.SymmGroup class method) from_subunit_motl() (cryocat.analysis.assembly.CnComplex class method) from_vectors() (cryocat.utils.geom.Polyhedron class method) fsc_read() (in module cryocat.utils.ioutils) fsc_write() (in module cryocat.utils.ioutils) full_participation (cryocat.analysis.sta.CoassignmentFactor property) G gamma (cryocat.utils.imod.ModelHeader attribute) gather_case_results() (in module cryocat.analysis.pana) gaussian_smooth() (in module cryocat.utils.imageutils) gaussian_threshold() (in module cryocat.utils.imageutils) gctf_read() (in module cryocat.utils.ioutils) generate_angles() (in module cryocat.utils.geom) generate_command_line() (in module cryocat.utils.scriptutils) generate_ctf_slice() (in module cryocat.utils.imageutils) generate_interactive_command() (in module cryocat.utils.scriptutils) generate_mask() (in module cryocat.core.cryomask) generate_matching_statistics() (in module cryocat.analysis.memthick) generate_python_command() (in module cryocat.utils.scriptutils) generate_rotated_axes() (cryocat.analysis.tango.SHOTDescriptor method) generate_script() (in module cryocat.utils.scriptutils) generate_wedge_mask() (in module cryocat.core.cryowedge) GeodesicDistNN (class in cryocat.analysis.tango) GeodesicnDistStatsTwist (class in cryocat.analysis.tango) get() (cryocat.analysis.sta.StaParamContext method) 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_assembly_stats() (cryocat.analysis.assembly.PleomorphicSurface method) get_axis_feature_id() (cryocat.analysis.tango.TwistDescriptor static method) get_axis_from_rotation() (in module cryocat.utils.geom) get_barycentric_motl() (cryocat.analysis.nnana.NearestNeighbors method) (cryocat.core.cryomotl.Motl method) get_block_stats() (cryocat.analysis.assembly.PleomorphicSurface method) get_blocks_as_motl() (cryocat.analysis.assembly.PleomorphicSurface method) get_bond_elevations() (cryocat.analysis.assembly.PleomorphicSurface method) get_bounding_box() (in module cryocat.core.cryomask) get_centers_as_motl() (cryocat.analysis.assembly.CnComplex method) (cryocat.analysis.assembly.NPC static method) (cryocat.analysis.assembly.SymmetricComplex method) get_central_label() (in module cryocat.analysis.tmana) get_central_plane_labels() (in module cryocat.analysis.tmana) get_centre_comparison() (cryocat.analysis.assembly.CnComplex method) get_chain_stats() (cryocat.analysis.assembly.Chain method) get_choices() (in module cryocat.analysis.sta) get_class_chain_occupancies() (cryocat.analysis.assembly.Chain method) get_class_names_by_parent() (in module cryocat.utils.classutils) get_class_names_by_prefix() (in module cryocat.utils.classutils) get_class_occupancy() (in module cryocat.analysis.sta) get_classes_from_names() (in module cryocat.utils.classutils) get_component_stats() (cryocat.analysis.assembly.CnComplex method) get_connected_component_count() (cryocat.core.surface.Mesh method) get_connected_triangles() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_contact_stats() (cryocat.analysis.assembly.PleomorphicSurface method) get_coordinates() (cryocat.core.cryomotl.Motl method) get_cross_slices() (in module cryocat.core.cryomap) get_curvature_directions() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_curvature_table() (cryocat.core.surface.Mesh method) get_curvature_tensors() (cryocat.core.surface.Mesh method) get_curvedness() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_data_from_warp_xml() (in module cryocat.utils.ioutils) get_data_range() (cryocat.analysis.tango.TwistDescriptor class method) get_default() (in module cryocat.analysis.sta) get_ellipsoid_label() (in module cryocat.analysis.tmana) get_euler_characteristic() (cryocat.core.surface.Mesh method) get_face_filling_summary() (cryocat.analysis.assembly.PleomorphicSurface method) get_face_inference() (cryocat.analysis.assembly.PleomorphicSurface method) get_face_stats() (cryocat.analysis.assembly.PleomorphicSurface method) get_face_vertices_as_motl() (cryocat.analysis.assembly.PleomorphicSurface method) get_faces_as_motl() (cryocat.analysis.assembly.PleomorphicSurface method) get_feature() (cryocat.core.cryomotl.Motl method) get_feature_nn_indices() (in module cryocat.analysis.nnana) 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) (in module cryocat.utils.imageutils) get_frame_and_comments() (cryocat.utils.starfileio.Starfile static method) get_fsc_filename() (cryocat.analysis.sta.NovaStaParams method) get_gaps_as_motl() (cryocat.analysis.assembly.PleomorphicSurface method) get_gaussian_curvature() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_half_map_paths() (cryocat.analysis.sta.NovaStaParams method) (cryocat.analysis.sta.StopgapParams 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_inverted_blocks() (cryocat.analysis.assembly.PleomorphicSurface method) get_inverted_blocks_as_motl() (cryocat.analysis.assembly.PleomorphicSurface method) get_label_bounding_box() (in module cryocat.utils.imageutils) 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_mean_curvature() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_metadata() (in module cryocat.core.cryomap) get_missing_block_motl() (cryocat.analysis.assembly.PleomorphicSurface method) get_mixed_feature_ids() (cryocat.analysis.tango.TwistDescriptor static method) get_motl_base_name() (cryocat.analysis.sta.StaParameters method) (cryocat.analysis.sta.StopgapParams method) 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_neighboring_triangles() (cryocat.analysis.assembly.PleomorphicSurface method) get_nn_distances() (in module cryocat.analysis.nnana) get_nn_rotations() (cryocat.analysis.nnana.NearestNeighbors method) (in module cryocat.analysis.nnana) get_nn_stats() (in module cryocat.analysis.nnana) 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_normals() (cryocat.core.surface.DiscreteSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) get_number_of_digits() (in module cryocat.utils.mathutils) get_number_of_lines_with_character() (in module cryocat.utils.ioutils) get_object_stats() (cryocat.analysis.assembly.CnComplex method) (cryocat.analysis.assembly.DnComplex method) (cryocat.analysis.assembly.NPC method) get_occupancy() (cryocat.analysis.assembly.Chain method) get_pixel_indices() (cryocat.core.surface.Mesh method) get_point_neighborhoods() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.OrientedPointCloud method) get_points_within_distance() (cryocat.analysis.assembly.PleomorphicSurface method) get_pore_frame_coords() (cryocat.analysis.assembly.CnComplex method) get_pos_feature_ids() (cryocat.analysis.tango.TwistDescriptor static method) get_principal_curvatures() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_props_as_df() (cryocat.core.surface.Ellipsoid method) get_props_as_dict() (cryocat.core.surface.Ellipsoid method) get_props_as_list() (cryocat.core.surface.Ellipsoid method) get_props_as_ndarray() (cryocat.core.surface.Ellipsoid 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_relative_rotations() (cryocat.analysis.nnana.NearestNeighbors method) get_required_columns() (cryocat.analysis.nnana.NearestNeighbors class method) get_rot_feature_ids() (cryocat.analysis.tango.TwistDescriptor static method) get_rotated_coord() (cryocat.analysis.nnana.NearestNeighbors method) get_rotations() (cryocat.core.cryomotl.Motl method) get_schema() (in module cryocat.analysis.sta) get_shape_index() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_shape_stats() (cryocat.analysis.assembly.PleomorphicSurface method) (in module cryocat.analysis.pana) get_shared_schema() (in module cryocat.analysis.sta) get_similar_size_factors() (in module cryocat.utils.mathutils) get_sites_as_motl() (cryocat.analysis.assembly.PleomorphicSurface method) 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_step_stats() (cryocat.analysis.assembly.Chain method) get_subtomos_class_stability() (in module cryocat.analysis.sta) get_subunit_orientation() (cryocat.analysis.assembly.NPC method) get_subunit_spacing() (cryocat.analysis.assembly.NPC method) get_subunit_stats() (cryocat.analysis.assembly.NPC method) get_surface_area() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_surface_type() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) get_symm_parameters() (cryocat.analysis.tango.TwistDescriptor static method) get_symmetry_angles() (in module cryocat.utils.symmetry) get_symmetry_rotations() (in module cryocat.utils.symmetry) get_tilt_angles() (in module cryocat.core.mdoc) get_triangle_neighborhoods() (cryocat.analysis.assembly.PleomorphicSurface method) get_triangles_within_radius() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) 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) get_vertices() (cryocat.core.surface.DiscreteSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) great_circle_distance() (in module cryocat.utils.geom) great_circle_distance_matrix() (in module cryocat.utils.geom) green (cryocat.utils.imod.ObjectHeader attribute) group (cryocat.analysis.sta.StaParamSpec attribute) (cryocat.utils.classutils.GuiEntry attribute) group_sizes (cryocat.analysis.sta.ConsensusResult attribute) gui_exposed() (in module cryocat.utils.classutils) GUI_REGISTRY (in module cryocat.utils.classutils) GuiCategory (class in cryocat.utils.classutils) GuiEntry (class in cryocat.utils.classutils) H has_blocks (cryocat.analysis.assembly.PleomorphicSurface property) has_envelope (cryocat.analysis.assembly.PleomorphicSurface property) has_envelopes (cryocat.analysis.assembly.PleomorphicSurface property) hausdorff_distance_sphere() (in module cryocat.utils.geom) header_format (cryocat.utils.imod.ContourHeader attribute) (cryocat.utils.imod.ImodHeader attribute) (cryocat.utils.imod.ModelHeader attribute) (cryocat.utils.imod.ObjectHeader attribute) height (cryocat.analysis.visplot.Defaults attribute) hide (cryocat.utils.classutils.GuiEntry attribute) highpass() (in module cryocat.core.cryomap) Hist2DBuilder (class in cryocat.analysis.visplot) HistBuilder (class in cryocat.analysis.visplot) I icosahedral_mask() (in module cryocat.core.cryomask) IcosahedralComplex (class in cryocat.analysis.assembly) IcosahedralGroup (class in cryocat.utils.symmetry) Icosahedron (class in cryocat.utils.geom) identity() (cryocat.analysis.tango.Particle class method) imod_com_read() (in module cryocat.utils.ioutils) ImodHeader (class in cryocat.utils.imod) in_box_bounds() (in module cryocat.utils.geom) in_plane_angle() (cryocat.analysis.tango.Particle method) (cryocat.utils.geom.Matrix method) indicator() (cryocat.analysis.sta.CoassignmentFactor method) indices_load() (in module cryocat.utils.ioutils) indices_reset() (in module cryocat.utils.ioutils) infer_missing_blocks() (cryocat.analysis.assembly.PleomorphicSurface method) inherit_coordinate_metadata() (cryocat.core.surface.Surface method) inner_angles() (cryocat.utils.geom.Triangle method) inplane_angle_after_alignment() (in module cryocat.utils.geom) inplane_distance() (in module cryocat.utils.geom) input_motl_id (cryocat.analysis.sta.StaRun attribute) inscribed_circle() (cryocat.utils.geom.Triangle method) IntensityProfileAnalyzer (class in cryocat.analysis.memthick) inter_ring_twist() (cryocat.analysis.assembly.DnComplex method) (cryocat.analysis.assembly.NPC method) interior_angle (cryocat.analysis.assembly.CnComplex property) interp() (cryocat.utils.ioutils.CubicGrid method) (cryocat.utils.ioutils.LinearGrid4D method) intersection() (in module cryocat.core.cryomask) intersection_data() (cryocat.analysis.assembly.PleomorphicSurface method) intersection_line() (cryocat.core.surface.Ellipsoid method) intersection_line_segment() (cryocat.core.surface.Ellipsoid method) intersection_ray() (cryocat.core.surface.Ellipsoid method) inv() (cryocat.analysis.tango.Particle method) invalidate_caches() (cryocat.analysis.assembly.PleomorphicSurface method) invert_contrast() (in module cryocat.core.cryomap) is_avg_row (cryocat.analysis.sta.StaParamContext attribute) is_float() (in module cryocat.utils.ioutils) is_mandatory() (in module cryocat.analysis.sta) is_mesh (cryocat.analysis.assembly.PleomorphicSurface property) is_point_cloud (cryocat.analysis.assembly.PleomorphicSurface property) is_SE3() (cryocat.utils.geom.Matrix method) is_SO3() (cryocat.utils.geom.Matrix method) is_surface_point() (in module cryocat.analysis.memthick) is_watertight() (cryocat.core.surface.Mesh method) J job (cryocat.analysis.sta.Block attribute) junk_class (cryocat.analysis.sta.ConsensusResult attribute) K k_distance_curve() (in module cryocat.analysis.clustering) 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) key (cryocat.utils.classutils.GuiEntry attribute) kind (cryocat.utils.classutils.GuiEntry attribute) kmeans_cluster() (in module cryocat.analysis.clustering) L label (cryocat.utils.classutils.GuiEntry attribute) label_at_point() (in module cryocat.utils.imageutils) label_connected_components() (in module cryocat.utils.imageutils) labels (cryocat.analysis.sta.CoassignmentFactor attribute) (cryocat.analysis.sta.ConsensusResult attribute) Line (class in cryocat.utils.geom) LinearGrid4D (class in cryocat.utils.ioutils) LineSegment (class in cryocat.utils.geom) linesty (cryocat.utils.imod.ObjectHeader attribute) linewidth (cryocat.utils.imod.ObjectHeader attribute) linewidth2 (cryocat.utils.imod.ObjectHeader attribute) linkage (cryocat.analysis.sta.ConsensusResult attribute) LinkTypeAlphaComplex (class in cryocat.analysis.tango) list_max() (cryocat.analysis.visplot.KDEBuilder method) LITERAL (cryocat.utils.starfileio.TokenType attribute) literals (cryocat.analysis.sta.StaParamSpec attribute) load() (cryocat.analysis.nnana.NearestNeighbors class method) (cryocat.analysis.sta.StaParameters class method) (cryocat.analysis.tango.CustomDescriptor class method) (cryocat.analysis.tango.TwistDescriptor class method) (cryocat.core.cryomotl.Motl class method) load_wedge_list_em() (in module cryocat.core.cryowedge) load_wedge_list_sg() (in module cryocat.core.cryowedge) load_xml_root() (in module cryocat.utils.ioutils) lookahead() (cryocat.utils.starfileio.Token static method) LOOP (cryocat.utils.starfileio.TokenType attribute) lowpass() (in module cryocat.core.cryomap) M make_angles_canonical() (cryocat.core.cryomotl.Motl method) mandatory_if (cryocat.analysis.sta.StaParamSpec attribute) map_tight_mask() (in module cryocat.core.cryomask) margin (cryocat.analysis.visplot.Defaults attribute) marker_coords_load() (in module cryocat.utils.ioutils) mask_overlap() (in module cryocat.core.cryomask) (in module cryocat.utils.imageutils) mask_stats() (in module cryocat.analysis.pana) mask_voxel_count_and_bbox() (in module cryocat.utils.imageutils) match_points() (in module cryocat.analysis.memthick) matrices (cryocat.utils.symmetry.SymmGroup attribute) Matrix (class in cryocat.utils.geom) matrix() (cryocat.analysis.sta.CoassignmentFactor method) matrix_power() (cryocat.utils.geom.Matrix method) max_angular_mismatch() (in module cryocat.utils.symmetry) max_dissimilarity() (cryocat.analysis.tango.SymmParticle method) Mdoc (class in cryocat.core.mdoc) measure_elements() (cryocat.analysis.assembly.CnComplex method) measure_thickness_cpu() (in module cryocat.analysis.memthick) measure_thickness_gpu() (in module cryocat.analysis.memthick) merge() (cryocat.analysis.assembly.NPC method) (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_objects() (cryocat.core.cryomotl.Motl method) merge_rings() (cryocat.analysis.assembly.NPC static method) merge_subunits() (cryocat.analysis.assembly.NPC method) (cryocat.analysis.assembly.SymmetricComplex method) Mesh (class in cryocat.core.surface) meshsize (cryocat.utils.imod.ObjectHeader attribute) method (cryocat.analysis.sta.ConsensusResult attribute) microtubule() (cryocat.analysis.assembly.BlockDefinition class method) min_agreement (cryocat.analysis.sta.ConsensusResult attribute) min_great_circle_distance() (in module cryocat.utils.geom) MixedDistNN (class in cryocat.analysis.tango) mod2emmotl() (in module cryocat.core.cryomotl) ModelHeader (class in cryocat.utils.imod) ModMotl (class in cryocat.core.cryomotl) module cryoCAT cryocat.analysis.assembly cryocat.analysis.clustering cryocat.analysis.memthick cryocat.analysis.nnana cryocat.analysis.pana cryocat.analysis.sta cryocat.analysis.tango cryocat.analysis.tmana cryocat.analysis.visplot cryocat.core.cryomap cryocat.core.cryomask cryocat.core.cryomotl cryocat.core.cryowedge cryocat.core.mdoc cryocat.core.surface cryocat.core.tiltstack cryocat.utils.classutils cryocat.utils.exceptions cryocat.utils.geom cryocat.utils.imageutils cryocat.utils.imod cryocat.utils.ioutils cryocat.utils.mathutils cryocat.utils.scriptutils cryocat.utils.starfileio cryocat.utils.symmetry molmap_tight_mask() (in module cryocat.core.cryomask) morphology_open_close() (in module cryocat.utils.imageutils) Motl (class in cryocat.core.cryomotl) motl_columns (cryocat.core.cryomotl.Motl attribute) motl_converter_kwargs() (in module cryocat.core.cryomotl) motl_name (cryocat.analysis.sta.Block attribute) MOTL_OP (cryocat.utils.classutils.GuiCategory attribute) motl_type (cryocat.analysis.sta.NovaStaParams property) (cryocat.analysis.sta.StaParameters property) (cryocat.analysis.sta.StopgapParams property) MotlException motls (cryocat.utils.classutils.GuiEntry attribute) mousemode (cryocat.utils.imod.ModelHeader attribute) mrc2em() (in module cryocat.core.cryomap) multiply_by_ctf() (in module cryocat.core.cryomap) N n_assigned (cryocat.analysis.sta.ConsensusResult attribute) n_classes (cryocat.analysis.sta.CoassignmentFactor attribute) n_edges (cryocat.utils.geom.Cube attribute) (cryocat.utils.geom.Dodecahedron attribute) (cryocat.utils.geom.Icosahedron attribute) (cryocat.utils.geom.Octahedron attribute) (cryocat.utils.geom.Polyhedron attribute) (cryocat.utils.geom.Tetrahedron attribute) n_faces (cryocat.utils.geom.Cube attribute) (cryocat.utils.geom.Dodecahedron attribute) (cryocat.utils.geom.Icosahedron attribute) (cryocat.utils.geom.Octahedron attribute) (cryocat.utils.geom.Polyhedron attribute) (cryocat.utils.geom.Tetrahedron attribute) n_gon_points() (in module cryocat.utils.geom) n_iterations (cryocat.analysis.sta.Block attribute) (cryocat.analysis.sta.StaParamContext attribute) n_junk (cryocat.analysis.sta.ConsensusResult attribute) n_particles (cryocat.analysis.sta.CoassignmentFactor property) n_runs (cryocat.analysis.sta.CoassignmentFactor property) (cryocat.analysis.sta.StaRun attribute) n_sites (cryocat.analysis.assembly.BlockDefinition property) n_vertices (cryocat.utils.geom.Cube attribute) (cryocat.utils.geom.Dodecahedron attribute) (cryocat.utils.geom.Icosahedron attribute) (cryocat.utils.geom.Octahedron attribute) (cryocat.utils.geom.Polyhedron attribute) (cryocat.utils.geom.Tetrahedron attribute) name (cryocat.utils.imod.ContourHeader attribute) (cryocat.utils.imod.ImodHeader attribute) (cryocat.utils.imod.ModelHeader attribute) (cryocat.utils.imod.ObjectHeader attribute) NearestNeighbors (class in cryocat.analysis.nnana) NEWLINE (cryocat.utils.starfileio.TokenType attribute) nms_by_distance() (in module cryocat.analysis.nnana) NNCountTwist (class in cryocat.analysis.tango) normal_deviations() (cryocat.analysis.assembly.SymmetricComplex method) normalize() (in module cryocat.core.cryomap) normalize_array() (in module cryocat.utils.imageutils) normalize_ranges() (cryocat.analysis.visplot.KDEBuilder method) normalize_under_mask() (in module cryocat.core.cryomap) (in module cryocat.utils.imageutils) normalize_vector() (in module cryocat.utils.geom) normalize_vectors() (in module cryocat.utils.geom) normals (cryocat.analysis.assembly.PleomorphicSurface property) normals_to_euler_angles() (in module cryocat.utils.geom) note (cryocat.analysis.sta.StaParamSpec attribute) nova_to_stopgap_angles() (in module cryocat.analysis.sta) novasta (cryocat.analysis.sta.StaParamSpec attribute) NovaStaParams (class in cryocat.analysis.sta) NPC (class in cryocat.analysis.assembly) num_iterations (cryocat.analysis.sta.StaParameters property) number_of_cone_rotations() (in module cryocat.utils.geom) O object (cryocat.utils.imod.ModelHeader attribute) ObjectHeader (class in cryocat.utils.imod) objsize (cryocat.utils.imod.ModelHeader attribute) occupancy() (cryocat.analysis.assembly.NPC method) (cryocat.analysis.assembly.SymmetricComplex method) OctahedralComplex (class in cryocat.analysis.assembly) OctahedralGroup (class in cryocat.utils.symmetry) Octahedron (class in cryocat.utils.geom) one_value_per_line_read() (in module cryocat.utils.ioutils) orbit() (cryocat.utils.symmetry.SymmGroup method) order (cryocat.utils.classutils.GuiEntry attribute) (cryocat.utils.symmetry.IcosahedralGroup attribute) (cryocat.utils.symmetry.OctahedralGroup attribute) (cryocat.utils.symmetry.SymmGroup attribute) (cryocat.utils.symmetry.TetrahedralGroup attribute) order_points_on_circle() (in module cryocat.utils.geom) ordered_pairs() (cryocat.analysis.nnana.NearestNeighbors static method) orient_normals_globally() (cryocat.core.surface.DiscreteSurface method) oriented() (cryocat.utils.symmetry.SymmGroup method) OrientedPointCloud (class in cryocat.core.surface) orthonormal_frame() (in module cryocat.utils.geom) otsu_threshold() (in module cryocat.utils.imageutils) output (cryocat.utils.classutils.GuiEntry attribute) output_base (cryocat.analysis.sta.StaRun attribute) overrides (cryocat.analysis.sta.Block attribute) oversample() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Cylinder method) (cryocat.core.surface.DiscreteSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) oversample_spline() (in module cryocat.utils.geom) owner (cryocat.utils.classutils.GuiEntry attribute) P pad() (in module cryocat.core.cryomap) pad_volume() (in module cryocat.utils.imageutils) padded_limits() (cryocat.analysis.visplot.KDEBuilder method) pairing (cryocat.analysis.assembly.BlockDefinition attribute) pairs (cryocat.core.cryomotl.StopgapMotl attribute) ParametricSurface (class in cryocat.analysis.assembly) params_to_template_row() (in module cryocat.analysis.pana) parse_column() (cryocat.utils.starfileio.Token static method) parse_columns() (cryocat.utils.starfileio.Token static method) parse_command() (in module cryocat.utils.scriptutils) parse_command_for_gui() (in module cryocat.utils.scriptutils) parse_newline_or_comments() (cryocat.utils.starfileio.Token static method) parse_rows() (cryocat.utils.starfileio.Token static method) parse_script_file() (in module cryocat.utils.scriptutils) 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) particle_ids (cryocat.analysis.sta.CoassignmentFactor attribute) (cryocat.analysis.sta.ConsensusResult attribute) path_arg (cryocat.utils.classutils.GuiEntry attribute) pca() (cryocat.analysis.sta.CoassignmentFactor method) pca_analysis() (cryocat.analysis.tango.Descriptor method) pca_feature_importance() (in module cryocat.analysis.clustering) pdrawsize (cryocat.utils.imod.ObjectHeader attribute) peak_shapes() (in module cryocat.analysis.pana) peak_stats_and_profiles() (in module cryocat.analysis.pana) per_element() (cryocat.analysis.assembly.CnComplex method) per_iteration (cryocat.analysis.sta.StaParamSpec attribute) per_ring() (cryocat.analysis.assembly.NPC method) pipeline_analysis_log_filename() (in module cryocat.analysis.memthick) pixel_size (cryocat.analysis.assembly.PleomorphicSurface property) (cryocat.core.surface.Surface attribute) pixels2resolution() (in module cryocat.core.cryomap) pixsize (cryocat.utils.imod.ModelHeader attribute) place_object() (in module cryocat.core.cryomap) PLComplexDescriptor (class in cryocat.analysis.tango) PLEOMORPHIC_OP (cryocat.utils.classutils.GuiCategory attribute) PleomorphicSurface (class in cryocat.analysis.assembly) 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_grouped_box() (in module cryocat.analysis.visplot) plot_histogram() (in module cryocat.analysis.visplot) plot_histogram_2d() (in module cryocat.analysis.visplot) plot_k_means() (cryocat.analysis.tango.Descriptor method) plot_kde() (in module cryocat.analysis.visplot) plot_line() (in module cryocat.analysis.visplot) plot_object() (cryocat.analysis.assembly.PleomorphicSurface method) plot_orientational_distribution() (in module cryocat.analysis.visplot) plot_otsu_thresholds() (in module cryocat.analysis.visplot) plot_pca_summary() (in module cryocat.analysis.visplot) plot_ply_mesh() (in module cryocat.analysis.visplot) plot_points_with_normals() (in module cryocat.analysis.visplot) plot_polar_nn_distances() (in module cryocat.analysis.visplot) plot_rotation_normals() (in module cryocat.analysis.visplot) plot_rotation_normals_binned() (in module cryocat.analysis.visplot) plot_scatter_2d() (in module cryocat.analysis.visplot) plot_scatter_3d() (in module cryocat.analysis.visplot) plot_scatter_with_histogram() (in module cryocat.analysis.visplot) plot_scatter_xyz_panels() (in module cryocat.analysis.visplot) plot_scores_and_peaks() (in module cryocat.analysis.visplot) 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_2d() (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) plot_vtp_mesh() (in module cryocat.analysis.visplot) point (cryocat.utils.imod.ModelHeader attribute) Point3D (class in cryocat.utils.geom) point_ellipsoid_distance() (in module cryocat.utils.geom) point_inside_triangle() (in module cryocat.utils.geom) point_pairwise_dist() (in module cryocat.utils.geom) PolyhedralComplex (class in cryocat.analysis.assembly) Polyhedron (class in cryocat.utils.geom) postprocess() (in module cryocat.core.cryomask) preflight_run_folder() (in module cryocat.analysis.sta) 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) presence() (cryocat.analysis.sta.CoassignmentFactor method) preview (cryocat.utils.classutils.GuiEntry attribute) print_summary() (in module cryocat.analysis.memthick) process_cluster_params() (in module cryocat.utils.scriptutils) 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_method_docstring() (in module cryocat.utils.classutils) process_second_axis_data() (cryocat.analysis.visplot.BaseBuilder method) process_tomo_twist() (cryocat.analysis.tango.TwistDescriptor static method) process_warp_subtomos() (in module cryocat.analysis.sta) ProcessError project() (in module cryocat.utils.geom) 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.utils.geom) project_lambert() (in module cryocat.utils.geom) project_parts() (in module cryocat.utils.geom) project_points_on_plane_with_preserved_distance() (in module cryocat.utils.geom) project_points_on_sphere() (in module cryocat.utils.geom) project_px() (in module cryocat.utils.geom) project_stereo() (in module cryocat.utils.geom) PROPERTY (cryocat.utils.starfileio.TokenType attribute) proximity_clustering() (cryocat.analysis.tango.Descriptor method) psize (cryocat.utils.imod.ContourHeader attribute) px_defaults() (in module cryocat.analysis.visplot) Q QuadricsM (class in cryocat.core.surface) quaternion_log() (in module cryocat.utils.geom) quaternion_mult() (in module cryocat.utils.geom) R random() (cryocat.analysis.tango.Particle class method) randomize_angles() (cryocat.core.cryomotl.Motl method) randomize_phases() (in module cryocat.utils.imageutils) ray_ellipsoid_intersection_3d() (in module cryocat.utils.geom) ray_hit_orientations() (cryocat.core.surface.DiscreteSurface static method) ray_intersections() (cryocat.analysis.assembly.PleomorphicSurface method) ray_ray_intersection_3d() (in module cryocat.utils.geom) rays_from_motl() (in module cryocat.analysis.assembly) read() (cryocat.analysis.assembly.PleomorphicSurface class method) (cryocat.core.surface.Mesh class method) (cryocat.core.surface.OrientedPointCloud class method) (cryocat.utils.starfileio.Starfile static method) (in module cryocat.core.cryomap) read_curvatures() (cryocat.core.surface.Mesh class method) read_from_file() (cryocat.utils.imod.ImodHeader class method) 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_mod_file() (in module cryocat.utils.imod) read_mod_files() (in module cryocat.utils.imod) read_warp_tilt_xml() (in module cryocat.utils.ioutils) READER (cryocat.utils.classutils.GuiCategory attribute) recenter() (in module cryocat.core.cryomap) recenter_to_subparticle() (cryocat.core.cryomotl.Motl static method) recenter_volume() (in module cryocat.utils.imageutils) recompute_dist_maps() (in module cryocat.analysis.pana) recover_columns_by_coordinates() (in module cryocat.analysis.nnana) recover_features() (cryocat.analysis.assembly.PolyhedralComplex class method) recover_orientations() (cryocat.analysis.assembly.PleomorphicSurface method) red (cryocat.utils.imod.ObjectHeader attribute) reduce_angle_grid() (in module cryocat.utils.symmetry) ref_family (cryocat.analysis.sta.StaParamContext attribute) references (cryocat.analysis.sta.StaRun attribute) refine_normals() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.DiscreteSurface method) refine_normals_from_arrays() (cryocat.core.surface.DiscreteSurface static method) register_colorscale() (in module cryocat.analysis.visplot) register_palette() (in module cryocat.analysis.visplot) regroup_objects() (cryocat.analysis.assembly.PleomorphicSurface method) relative_rotations() (in module cryocat.analysis.nnana) reliability_summary() (in module cryocat.analysis.sta) reliable (cryocat.analysis.sta.ConsensusResult attribute) 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) remap_warp_alignment() (cryocat.core.cryomotl.Motl method) remove_boundary_vertices() (cryocat.core.surface.Mesh method) remove_disconnected_components() (cryocat.core.surface.Mesh method) 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_images_by_angles() (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_nonfinite_vertices() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.DiscreteSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud 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) removed_tilts_load() (in module cryocat.utils.ioutils) 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) renumber_subunits() (cryocat.analysis.assembly.CnComplex method) reorder_images() (cryocat.core.mdoc.Mdoc method) replace_command_in_script() (in module cryocat.utils.scriptutils) require_cyclic_symmetry() (in module cryocat.utils.geom) res (cryocat.utils.imod.ModelHeader attribute) reset_images() (cryocat.core.mdoc.Mdoc method) resolution2pixels() (in module cryocat.core.cryomap) resolve_ccmask() (cryocat.analysis.sta.NovaStaParams method) (cryocat.analysis.sta.StopgapParams method) resolve_colors_any() (in module cryocat.analysis.visplot) resolve_colorscale() (in module cryocat.analysis.visplot) resolve_mask() (cryocat.analysis.sta.NovaStaParams method) (cryocat.analysis.sta.StopgapParams method) resolve_palette() (in module cryocat.analysis.visplot) resolve_param_type() (in module cryocat.utils.classutils) resolve_ref_base() (cryocat.analysis.sta.NovaStaParams method) (cryocat.analysis.sta.StopgapParams method) resolve_symmetry_argument() (in module cryocat.utils.geom) resolve_wedge_list() (cryocat.analysis.sta.NovaStaParams method) (cryocat.analysis.sta.StopgapParams method) restore_affiliation() (cryocat.analysis.assembly.CnComplex method) returns (cryocat.utils.classutils.GuiEntry attribute) ring_ellipticity() (cryocat.analysis.assembly.NPC method) ring_spacing() (cryocat.analysis.assembly.DnComplex method) (cryocat.analysis.assembly.NPC method) ring_summary() (cryocat.analysis.assembly.CnComplex method) RotAngleXStatsTwist (class in cryocat.analysis.tango) RotAngleYStatsTwist (class in cryocat.analysis.tango) RotAngleZStatsTwist (class in cryocat.analysis.tango) rotate() (cryocat.core.surface.AnalyticSurface method) (cryocat.core.surface.Cylinder method) (cryocat.core.surface.Ellipsoid method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) (cryocat.core.surface.Surface method) (in module cryocat.core.cryomap) (in module cryocat.core.cryomask) rotate_2d() (in module cryocat.utils.imageutils) rotate_points_rodrigues() (in module cryocat.utils.geom) rotate_vectors_about_axis() (in module cryocat.utils.geom) rotate_volume() (in module cryocat.utils.imageutils) rotated_nn_coords() (in module cryocat.analysis.nnana) rotation (cryocat.utils.symmetry.SymmGroup attribute) rotations_to_unit_vectors() (in module cryocat.analysis.nnana) rotations_to_z_normals() (in module cryocat.utils.geom) run_agreement() (cryocat.analysis.sta.CoassignmentFactor method) run_analysis() (in module cryocat.analysis.pana) run_angle_analysis() (in module cryocat.analysis.pana) run_full_pipeline() (in module cryocat.analysis.memthick) run_labels (cryocat.analysis.sta.CoassignmentFactor attribute) run_mode (cryocat.analysis.sta.StaRun attribute) run_single_case() (in module cryocat.analysis.pana) run_single_gradual_case() (in module cryocat.analysis.pana) S sample_along_axis() (cryocat.core.surface.Cylinder method) sample_along_axis_spline() (cryocat.core.surface.Cylinder method) sample_cone() (in module cryocat.utils.geom) sample_line_profiles() (in module cryocat.core.cryomap) sample_points_poisson_disk() (cryocat.core.surface.Mesh method) sample_sphere() (in module cryocat.utils.geom) sample_triangle() (in module cryocat.utils.geom) save() (cryocat.analysis.assembly.PleomorphicSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) save_as_svg() (in module cryocat.analysis.visplot) save_int_results() (in module cryocat.analysis.memthick) save_matching_statistics() (in module cryocat.analysis.memthick) save_per_surface_mrc_helper() (in module cryocat.analysis.memthick) save_thickness_volume_mrc() (in module cryocat.analysis.memthick) save_to() (cryocat.core.cryomotl.Motl method) save_vertices_csv() (cryocat.core.surface.Mesh method) save_vertices_mrc() (cryocat.core.surface.Mesh method) scale() (cryocat.analysis.tango.Particle method) (in module cryocat.core.cryomap) scale_coordinates() (cryocat.core.cryomotl.Motl method) ScatterBuilder (class in cryocat.analysis.visplot) schedule (cryocat.analysis.sta.StaRun attribute) scores_extract_particles() (in module cryocat.analysis.tmana) scores_extract_particles_around_positions() (in module cryocat.analysis.tmana) screen_feature_columns() (in module cryocat.analysis.clustering) SE3_cleanup() (cryocat.utils.geom.Matrix method) search_mode (cryocat.analysis.sta.Block attribute) select_peaks() (in module cryocat.analysis.tmana) separate_closed_surface() (cryocat.core.surface.DiscreteSurface method) separate_planar_surface() (cryocat.core.surface.DiscreteSurface method) separate_surfaces() (cryocat.analysis.assembly.PleomorphicSurface 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) set_volume_geometry() (in module cryocat.utils.ioutils) setup_logger() (in module cryocat.analysis.memthick) sg_df_reset_index() (cryocat.core.cryomotl.StopgapMotl static method) shape_stats() (in module cryocat.analysis.pana) sharp_mask_overlap() (in module cryocat.analysis.pana) Shell (class in cryocat.analysis.tango) shift() (in module cryocat.core.cryomap) shift_array() (in module cryocat.utils.imageutils) 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) simplify() (cryocat.core.surface.Mesh method) site_type (cryocat.analysis.assembly.ContactSite attribute) site_types (cryocat.analysis.assembly.BlockDefinition property) site_vectors() (cryocat.analysis.assembly.BlockDefinition method) sites (cryocat.analysis.assembly.BlockDefinition attribute) smooth() (cryocat.core.surface.Mesh method) solid (cryocat.analysis.assembly.PolyhedralComplex attribute) 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_by_ring() (cryocat.analysis.assembly.NPC method) split_in_asymmetric_subunits() (cryocat.core.cryomotl.Motl method) split_in_asymmetric_units() (cryocat.analysis.assembly.PolyhedralComplex method) split_mdoc_file() (in module cryocat.core.mdoc) split_rings() (cryocat.analysis.assembly.DnComplex method) split_stack_even_odd() (in module cryocat.core.tiltstack) sta_log_read() (in module cryocat.analysis.sta) sta_type (cryocat.analysis.sta.StaParamContext attribute) standalone (cryocat.utils.classutils.GuiEntry attribute) StaParamContext (class in cryocat.analysis.sta) StaParameters (class in cryocat.analysis.sta) StaParamSpec (class in cryocat.analysis.sta) Starfile (class in cryocat.utils.starfileio) start_iteration (cryocat.analysis.sta.StaParameters property) StaRun (class in cryocat.analysis.sta) step_statistics() (cryocat.analysis.assembly.NPC method) stopgap (cryocat.analysis.sta.StaParamSpec attribute) stopgap2emmotl() (in module cryocat.core.cryomotl) stopgap2relion() (in module cryocat.core.cryomotl) stopgap_to_nova_angles() (in module cryocat.analysis.sta) StopgapMotl (class in cryocat.core.cryomotl) StopgapParams (class in cryocat.analysis.sta) store_block_stat() (cryocat.analysis.assembly.PleomorphicSurface method) store_block_stats() (cryocat.analysis.assembly.PleomorphicSurface method) subdivide_mesh() (cryocat.core.surface.Mesh method) subtomo_path (cryocat.analysis.sta.StaRun attribute) subtraction() (in module cryocat.core.cryomask) suggest_alpha_range() (cryocat.core.surface.Mesh static method) Support (class in cryocat.analysis.tango) SupportCatalog (class in cryocat.analysis.tango) surf (cryocat.utils.imod.ContourHeader attribute) Surface (class in cryocat.core.surface) surface (cryocat.analysis.assembly.PleomorphicSurface property) SURFACE_LOAD (cryocat.utils.classutils.GuiCategory attribute) SURFACE_OP (cryocat.utils.classutils.GuiCategory attribute) SURFACE_TYPE_LABELS (cryocat.core.surface.Mesh attribute) surfsize (cryocat.utils.imod.ObjectHeader attribute) symbol (cryocat.utils.imod.ObjectHeader attribute) (cryocat.utils.symmetry.CyclicGroup attribute) (cryocat.utils.symmetry.DihedralGroup attribute) (cryocat.utils.symmetry.IcosahedralGroup attribute) (cryocat.utils.symmetry.OctahedralGroup attribute) (cryocat.utils.symmetry.SymmGroup attribute) (cryocat.utils.symmetry.TetrahedralGroup attribute) symflags (cryocat.utils.imod.ObjectHeader attribute) SymmetricComplex (class in cryocat.analysis.assembly) symmetrize_volume() (in module cryocat.core.cryomap) (in module cryocat.utils.imageutils) symmetry (cryocat.analysis.assembly.BlockDefinition attribute) symmetry_group() (cryocat.analysis.assembly.PolyhedralComplex method) symmetry_statistics() (cryocat.analysis.tango.TwistDescriptor method) SymmGroup (class in cryocat.utils.symmetry) SymmParticle (class in cryocat.analysis.tango) sympad (cryocat.utils.imod.ObjectHeader attribute) symsize (cryocat.utils.imod.ObjectHeader attribute) T tangent_at_identity() (cryocat.analysis.tango.Particle method) tangent_subspace_projection() (cryocat.analysis.tango.Particle method) temperature (cryocat.analysis.sta.Block attribute) template (cryocat.analysis.visplot.Defaults attribute) TetrahedralComplex (class in cryocat.analysis.assembly) TetrahedralGroup (class in cryocat.utils.symmetry) Tetrahedron (class in cryocat.utils.geom) thresh (cryocat.utils.imod.ModelHeader attribute) TiltStack (class in cryocat.core.tiltstack) time (cryocat.utils.imod.ContourHeader attribute) tlt_load() (in module cryocat.utils.ioutils) to_bytes() (cryocat.utils.imod.ContourHeader method) (cryocat.utils.imod.ModelHeader method) (cryocat.utils.imod.ObjectHeader method) to_format (cryocat.analysis.sta.StaParamSpec attribute) to_layout_kwargs() (cryocat.analysis.visplot.Defaults method) to_motl() (cryocat.core.surface.OrientedPointCloud method) to_novasta() (cryocat.analysis.sta.StaParameters method) to_oriented_points() (cryocat.core.surface.Mesh method) to_polyhedron() (cryocat.utils.symmetry.SymmGroup method) to_segmentation() (cryocat.core.surface.Mesh method) to_stats_dataframe() (cryocat.analysis.nnana.NearestNeighbors method) to_stopgap() (cryocat.analysis.sta.StaParameters 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.nnana) trace_faces() (in module cryocat.analysis.assembly) trans (cryocat.utils.imod.ObjectHeader attribute) transform() (cryocat.core.surface.AnalyticSurface method) (cryocat.core.surface.Cylinder method) (cryocat.core.surface.Ellipsoid method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) (cryocat.core.surface.Surface method) translate() (cryocat.core.surface.AnalyticSurface method) (cryocat.core.surface.Mesh method) (cryocat.core.surface.OrientedPointCloud method) (cryocat.core.surface.Surface method) translate_along_normals() (cryocat.core.surface.OrientedPointCloud method) transport_points() (cryocat.utils.geom.Polyhedron method) Triangle (class in cryocat.utils.geom) triangle_sizes() (cryocat.core.surface.Mesh method) triangle_threshold() (in module cryocat.utils.imageutils) triangulate() (in module 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.assembly.NPC method) unify_polarity() (cryocat.analysis.assembly.PleomorphicSurface method) union() (in module cryocat.core.cryomask) unit_axis() (in module cryocat.utils.geom) units (cryocat.analysis.assembly.PleomorphicSurface property) (cryocat.core.surface.Surface attribute) (cryocat.utils.imod.ModelHeader attribute) 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_ring_motls() (cryocat.analysis.assembly.NPC method) use_defaults() (in module cryocat.analysis.visplot) use_euler_search (cryocat.analysis.sta.StaParamContext attribute) UserInputError V validate() (cryocat.analysis.sta.StaParameters method) validate_ref_mapping() (in module cryocat.analysis.sta) validate_seg_tomo_compatibility() (in module cryocat.analysis.memthick) vector (cryocat.analysis.assembly.ContactSite attribute) vector_angular_distance() (in module cryocat.utils.geom) vector_angular_distance_signed() (in module cryocat.utils.geom) verdict (cryocat.analysis.sta.ConsensusResult attribute) verify_and_save_outputs() (in module cryocat.analysis.memthick) vertex_neighbors() (cryocat.utils.geom.Polyhedron method) vertex_subunit_vectors() (cryocat.analysis.assembly.PolyhedralComplex method) vertices (cryocat.analysis.assembly.PleomorphicSurface property) visualize_results() (in module cryocat.analysis.pana) W warp2relion() (cryocat.core.cryomotl.RelionMotlv5 method) warp_ctf_read() (in module cryocat.utils.ioutils) wedge_list_sg_to_em() (in module cryocat.core.cryowedge) weighted_stats() (cryocat.analysis.tango.TwistDescriptor method) whitelevel (cryocat.utils.imod.ModelHeader attribute) width (cryocat.analysis.visplot.Defaults attribute) write() (cryocat.core.mdoc.Mdoc method) (cryocat.utils.starfileio.Starfile static method) (in module cryocat.core.cryomap) write_coords_to_cmm_file() (in module cryocat.utils.ioutils) write_features_cmm() (cryocat.analysis.assembly.PolyhedralComplex method) write_hdf5() (in module cryocat.core.cryomap) write_model_binary() (in module cryocat.utils.imod) write_out() (cryocat.analysis.assembly.ParametricSurface method) (cryocat.analysis.nnana.NearestNeighbors method) (cryocat.analysis.sta.NovaStaParams method) (cryocat.analysis.sta.StopgapParams method) (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.surface.QuadricsM method) (cryocat.core.tiltstack.TiltStack method) (in module cryocat.core.cryomask) write_out_motl() (in module cryocat.analysis.sta) write_ring_motls() (cryocat.analysis.assembly.NPC method) write_to_model_file() (cryocat.core.cryomotl.Motl method) X x (cryocat.utils.geom.Point3D property) xmax (cryocat.utils.imod.ModelHeader attribute) xoffset (cryocat.utils.imod.ModelHeader attribute) xscale (cryocat.utils.imod.ModelHeader attribute) Y y (cryocat.utils.geom.Point3D property) ymax (cryocat.utils.imod.ModelHeader attribute) yoffset (cryocat.utils.imod.ModelHeader attribute) yscale (cryocat.utils.imod.ModelHeader attribute) Z z (cryocat.utils.geom.Point3D property) z_shift_load() (in module cryocat.utils.ioutils) zmax (cryocat.utils.imod.ModelHeader attribute) zoffset (cryocat.utils.imod.ModelHeader attribute) zscale (cryocat.utils.imod.ModelHeader attribute)