Index _ | A | B | C | D | E | F | G | H | I | L | M | N | P | Q | R | S | T | U | V | W | X | Y | Z _ __call__() (ConstantSchedule method) (CyclicalSchedule method) (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (LinearSchedule method) (MAB method) (MedianPool1d method) (Memoized method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) A add_args() (in module tomodrgn.commands.analyze) (in module tomodrgn.commands.analyze_volumes) (in module tomodrgn.commands.backproject_voxel) (in module tomodrgn.commands.cleanup) (in module tomodrgn.commands.convergence_nn) (in module tomodrgn.commands.convergence_vae) (in module tomodrgn.commands.downsample) (in module tomodrgn.commands.eval_images) (in module tomodrgn.commands.eval_vol) (in module tomodrgn.commands.filter_star) (in module tomodrgn.commands.graph_traversal) (in module tomodrgn.commands.pc_traversal) (in module tomodrgn.commands.subtomo2chimerax) (in module tomodrgn.commands.train_nn) (in module tomodrgn.commands.train_vae) (in module tomodrgn.commands.view_config) add_module() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) add_slice() (in module tomodrgn.commands.backproject_voxel) analyze_data_support() (in module tomodrgn.commands.pc_traversal) analyze_z_multidimensional() (in module tomodrgn.commands.analyze) analyze_z_onedimensional() (in module tomodrgn.commands.analyze) apply() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) B backproject_dataset() (in module tomodrgn.commands.backproject_voxel) base_SO3_grid() (in module tomodrgn.so3_grid) bfloat16() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) buffers() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) C calc_cc() (in module tomodrgn.utils) calc_ccs_alltoall_intraepoch() (in module tomodrgn.convergence) calc_ccs_alltogroundtruth() (in module tomodrgn.convergence) calc_ccs_pairwise_epochs() (in module tomodrgn.convergence) calc_fsc() (in module tomodrgn.utils) calc_fscs_pairwise_epochs() (in module tomodrgn.convergence) calc_kld_two_gaussians() (in module tomodrgn.convergence) calc_lowpass_filter_mask() (in module tomodrgn.utils) calc_real_space_mask() (in module tomodrgn.utils) calc_test_train_pair_volumes_cc_complement() (in module tomodrgn.convergence) calc_test_train_pair_volumes_fscs() (in module tomodrgn.convergence) calculate_critical_dose_per_frequency() (in module tomodrgn.dose) calculate_dose_mask() (in module tomodrgn.dose) calculate_dose_weights() (in module tomodrgn.dose) calculate_spatial_frequencies() (in module tomodrgn.dose) calculate_tilt_weights() (in module tomodrgn.dose) cat_z() (FTPositionalDecoder static method) check_args_compatible() (in module tomodrgn.commands.filter_star) check_git_revision_hash() (in module tomodrgn.utils) check_memory_usage() (in module tomodrgn.utils) children() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) cluster_gmm() (in module tomodrgn.analysis) cluster_kmeans() (in module tomodrgn.analysis) collate_particle_tilts() (in module tomodrgn.commands.downsample) combine_dose_tilt_weights() (in module tomodrgn.dose) combine_ind() (in module tomodrgn.analysis) compile() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) compute_ctf() (in module tomodrgn.ctf) ConstantSchedule (class in tomodrgn.beta_schedule) construct_from_array() (LatentGraph class method) convert_angstroms_to_voxels() (in module tomodrgn.analysis) convert_original_indices() (in module tomodrgn.analysis) cpu() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) cuda() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) CyclicalSchedule (class in tomodrgn.beta_schedule) D DataParallelPassthrough (class in tomodrgn.models) decode() (FTPositionalDecoder method) (TiltSeriesHetOnlyVAE method) decode_batch() (in module tomodrgn.commands.train_nn) (in module tomodrgn.commands.train_vae) df (TiltSeriesStarfile property) (TomoParticlesStarfile property) double() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) downsample_images() (in module tomodrgn.commands.downsample) E encode() (TiltSeriesHetOnlyVAE method) encode_batch() (in module tomodrgn.commands.train_vae) encoder_inference() (in module tomodrgn.commands.train_vae) encoder_latent_shifts() (in module tomodrgn.convergence) EquivarianceLoss (class in tomodrgn.losses) eval() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) eval_volume_batch() (FTPositionalDecoder method) EvenLattice (class in tomodrgn.lattice) expmap() (in module tomodrgn.lie_tools) extra_repr() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) F fft2_center() (in module tomodrgn.fft) fft2_center_torch() (in module tomodrgn.fft) fft3_center() (in module tomodrgn.fft) fft3_center_torch() (in module tomodrgn.fft) filter() (TiltSeriesStarfile method) (TomoParticlesStarfile method) filter_image_series_starfile() (in module tomodrgn.commands.filter_star) filter_volume_series_starfile() (in module tomodrgn.commands.filter_star) find_path_dijkstra() (LatentGraph method) first_n_factors() (in module tomodrgn.utils) float() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) flog() (in module tomodrgn.utils) follow_candidate_particles() (in module tomodrgn.convergence) forward() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) fsc_referencevol_to_manyvols() (in module tomodrgn.convergence) FTPositionalDecoder (class in tomodrgn.models) G generate_color_per_particle() (in module tomodrgn.commands.subtomo2chimerax) generate_test_train_pair_volumes() (in module tomodrgn.convergence) generate_volumes() (VolumeGenerator method) GenericStarfile (class in tomodrgn.starfile) get() (LazyImage method) (LazyImageStack method) get_apix() (MRCHeader method) get_base_ind() (in module tomodrgn.so3_grid) get_beta_schedule() (in module tomodrgn.beta_schedule) get_buffer() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) get_circular_mask() (Lattice method) get_colors_chimerax() (in module tomodrgn.analysis) get_colors_matplotlib() (in module tomodrgn.analysis) get_default_device() (in module tomodrgn.utils) get_downsample_coords() (Lattice method) get_extra_state() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) get_image_size() (TiltSeriesStarfile method) get_ind_for_cluster() (in module tomodrgn.analysis) get_latest_epoch() (in module tomodrgn.utils) get_nearest_point() (in module tomodrgn.analysis) get_neighbor() (in module tomodrgn.so3_grid) get_origin() (MRCHeader method) get_parameter() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) get_particles_stack() (GenericStarfile method) (TiltSeriesStarfile method) (TomoParticlesStarfile method) get_pc_traj() (in module tomodrgn.analysis) get_pose() (PoseTracker method) get_ptcl_img_indices() (TiltSeriesStarfile method) (TomoParticlesStarfile method) get_s1_neighbor() (in module tomodrgn.so3_grid) get_s2_neighbor() (in module tomodrgn.so3_grid) get_square_mask() (Lattice method) get_submodule() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) get_tiltseries_pixelsize() (TiltSeriesStarfile method) (TomoParticlesStarfile method) get_tiltseries_voltage() (TiltSeriesStarfile method) (TomoParticlesStarfile method) grid_s1() (in module tomodrgn.so3_grid) grid_s2() (in module tomodrgn.so3_grid) grid_SO3() (in module tomodrgn.so3_grid) H half() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) headers_ctf (TiltSeriesStarfile property) (TomoParticlesStarfile property) headers_rot (TiltSeriesStarfile property) (TomoParticlesStarfile property) headers_trans (TiltSeriesStarfile property) (TomoParticlesStarfile property) hopf_to_quat() (in module tomodrgn.so3_grid) ht2_center() (in module tomodrgn.fft) ht2_center_torch() (in module tomodrgn.fft) ht3_center() (in module tomodrgn.fft) ht3_center_torch() (in module tomodrgn.fft) I identify_particles_data_block() (GenericStarfile method) (TiltSeriesStarfile method) (TomoParticlesStarfile method) ifft2_center() (in module tomodrgn.fft) ifft2_center_torch() (in module tomodrgn.fft) ifft3_center() (in module tomodrgn.fft) ifft3_center_torch() (in module tomodrgn.fft) iht2_center() (in module tomodrgn.fft) iht2_center_torch() (in module tomodrgn.fft) iht3_center() (in module tomodrgn.fft) iht3_center_torch() (in module tomodrgn.fft) ImageDataset (class in tomodrgn.commands.downsample) ipu() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) ipy_plot_interactive() (in module tomodrgn.analysis) ipy_tomo_ptcl_viewer() (in module tomodrgn.analysis) is_starfile_optimisation_set() (in module tomodrgn.starfile) L LatentGraph (class in tomodrgn.commands.graph_traversal) Lattice (class in tomodrgn.lattice) lazy_particles_estimate_normalization() (TiltSeriesMRCData method) (TomoParticlesMRCData method) LazyImage (class in tomodrgn.mrc) LazyImageStack (class in tomodrgn.mrc) LinearSchedule (class in tomodrgn.beta_schedule) load() (FTPositionalDecoder class method) (PoseTracker class method) (TiltSeriesHetOnlyVAE class method) (TiltSeriesMRCData class method) (TomoParticlesMRCData class method) load_dataframe() (in module tomodrgn.analysis) load_particles() (in module tomodrgn.dataset) load_pkl() (in module tomodrgn.utils) load_sta_dataset() (in module tomodrgn.dataset) load_sta_starfile() (in module tomodrgn.starfile) load_state_dict() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) log() (in module tomodrgn.utils) logsumexp() (in module tomodrgn.lie_tools) loss_function() (in module tomodrgn.commands.train_nn) (in module tomodrgn.commands.train_vae) lowpass_filter() (in module tomodrgn.utils) M MAB (class in tomodrgn.set_transformer) main() (in module tomodrgn.commands.analyze) (in module tomodrgn.commands.analyze_volumes) (in module tomodrgn.commands.backproject_voxel) (in module tomodrgn.commands.cleanup) (in module tomodrgn.commands.convergence_nn) (in module tomodrgn.commands.convergence_vae) (in module tomodrgn.commands.downsample) (in module tomodrgn.commands.eval_images) (in module tomodrgn.commands.eval_vol) (in module tomodrgn.commands.filter_star) (in module tomodrgn.commands.graph_traversal) (in module tomodrgn.commands.pc_traversal) (in module tomodrgn.commands.subtomo2chimerax) (in module tomodrgn.commands.train_nn) (in module tomodrgn.commands.train_vae) (in module tomodrgn.commands.view_config) make_default_header() (MRCHeader class method) make_plots() (in module tomodrgn.commands.analyze_volumes) (in module tomodrgn.commands.convergence_nn) make_test_train_split() (TiltSeriesStarfile method) (TomoParticlesStarfile method) map_to_lie_algebra() (in module tomodrgn.lie_tools) MedianPool1d (class in tomodrgn.models) Memoized (class in tomodrgn.utils) mkbasedir() (in module tomodrgn.commands.downsample) mlp_ascii() (in module tomodrgn.models) module tomodrgn.analysis tomodrgn.beta_schedule tomodrgn.commands.analyze tomodrgn.commands.analyze_volumes tomodrgn.commands.backproject_voxel tomodrgn.commands.cleanup tomodrgn.commands.convergence_nn tomodrgn.commands.convergence_vae tomodrgn.commands.downsample tomodrgn.commands.eval_images tomodrgn.commands.eval_vol tomodrgn.commands.filter_star tomodrgn.commands.graph_traversal tomodrgn.commands.pc_traversal tomodrgn.commands.subtomo2chimerax tomodrgn.commands.train_nn tomodrgn.commands.train_vae tomodrgn.commands.view_config tomodrgn.config tomodrgn.convergence tomodrgn.ctf tomodrgn.dataset tomodrgn.dose tomodrgn.fft tomodrgn.lattice tomodrgn.lie_tools tomodrgn.losses tomodrgn.models tomodrgn.mrc tomodrgn.pose tomodrgn.set_transformer tomodrgn.so3_grid tomodrgn.starfile tomodrgn.utils modules() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) MRCHeader (class in tomodrgn.mrc) mtia() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) N named_buffers() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) named_children() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) named_modules() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) named_parameters() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) P parameters() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) parse() (MRCHeader class method) parse_all_losses() (in module tomodrgn.analysis) parse_header() (in module tomodrgn.mrc) parse_loss() (in module tomodrgn.analysis) parse_mrc() (in module tomodrgn.mrc) parse_mrc_list() (in module tomodrgn.mrc) plot_by_cluster() (in module tomodrgn.analysis) plot_by_cluster_subplot() (in module tomodrgn.analysis) plot_euler() (in module tomodrgn.analysis) plot_graph() (LatentGraph method) plot_label_count_distribution() (in module tomodrgn.analysis) plot_latent_pca() (in module tomodrgn.convergence) plot_latent_umap() (in module tomodrgn.convergence) plot_loss() (in module tomodrgn.convergence) plot_losses() (in module tomodrgn.analysis) plot_particle_uid_ntilt_distribution() (TiltSeriesStarfile method) (TomoParticlesStarfile method) plot_path() (LatentGraph method) plot_projections() (in module tomodrgn.analysis) plot_three_column_correlation() (in module tomodrgn.analysis) plot_translations() (in module tomodrgn.analysis) plot_weight_distribution() (in module tomodrgn.dose) PMA (class in tomodrgn.set_transformer) PoseTracker (class in tomodrgn.pose) positional_encoding() (FTPositionalDecoder method) postprocess_volume_batch() (FTPositionalDecoder static method) prefix_paths() (in module tomodrgn.utils) preprocess_batch() (in module tomodrgn.commands.train_vae) print_config() (in module tomodrgn.config) print_ctf_params() (in module tomodrgn.ctf) print_model_info() (TiltSeriesHetOnlyVAE method) print_progress_bar() (in module tomodrgn.utils) print_tiltserieshetonlyvae_ascii() (in module tomodrgn.models) Q quaternions_to_SO3() (in module tomodrgn.lie_tools) R random_quaternions() (in module tomodrgn.lie_tools) random_SO3() (in module tomodrgn.lie_tools) recursive_load_dataframe() (in module tomodrgn.analysis) register_backward_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_buffer() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_forward_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_forward_pre_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_full_backward_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_full_backward_pre_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_load_state_dict_post_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_load_state_dict_pre_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_module() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_parameter() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_state_dict_post_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) register_state_dict_pre_hook() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) reparameterize() (TiltSeriesEncoder method) requires_grad_() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) ResidLinear (class in tomodrgn.models) ResidLinearMLP (class in tomodrgn.models) rot_3d_from_eman() (in module tomodrgn.utils) rot_3d_from_relion() (in module tomodrgn.utils) rot_3d_from_relion_scipy() (in module tomodrgn.utils) rot_3d_to_relion_scipy() (in module tomodrgn.utils) rotate() (EquivarianceLoss method) (Lattice method) run_pca() (in module tomodrgn.analysis) run_tsne() (in module tomodrgn.analysis) run_umap() (in module tomodrgn.analysis) S s2s1rodrigues() (in module tomodrgn.lie_tools) s2s2_to_SO3() (in module tomodrgn.lie_tools) SAB (class in tomodrgn.set_transformer) save() (PoseTracker method) save_checkpoint() (in module tomodrgn.commands.train_nn) (in module tomodrgn.commands.train_vae) save_config() (in module tomodrgn.config) save_map() (in module tomodrgn.commands.backproject_voxel) save_pkl() (in module tomodrgn.utils) scatter_annotate() (in module tomodrgn.analysis) scatter_annotate_hex() (in module tomodrgn.analysis) scatter_color() (in module tomodrgn.analysis) set_extra_state() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) set_submodule() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) SetTransformer (class in tomodrgn.set_transformer) share_memory() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) sketch_via_umap_local_maxima() (in module tomodrgn.convergence) so3_entropy() (in module tomodrgn.lie_tools) so3_entropy_old() (in module tomodrgn.lie_tools) SO3_to_quaternions() (in module tomodrgn.lie_tools) SO3_to_s2s2() (in module tomodrgn.lie_tools) state_dict() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) symmetrize_ht() (in module tomodrgn.fft) T TiltSeriesEncoder (class in tomodrgn.models) TiltSeriesHetOnlyVAE (class in tomodrgn.models) TiltSeriesMRCData (class in tomodrgn.dataset) TiltSeriesStarfile (class in tomodrgn.starfile) TiltSeriesStarfileStarHeaders (class in tomodrgn.starfile) to() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) to_empty() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) tomodrgn.analysis module tomodrgn.beta_schedule module tomodrgn.commands.analyze module tomodrgn.commands.analyze_volumes module tomodrgn.commands.backproject_voxel module tomodrgn.commands.cleanup module tomodrgn.commands.convergence_nn module tomodrgn.commands.convergence_vae module tomodrgn.commands.downsample module tomodrgn.commands.eval_images module tomodrgn.commands.eval_vol module tomodrgn.commands.filter_star module tomodrgn.commands.graph_traversal module tomodrgn.commands.pc_traversal module tomodrgn.commands.subtomo2chimerax module tomodrgn.commands.train_nn module tomodrgn.commands.train_vae module tomodrgn.commands.view_config module tomodrgn.config module tomodrgn.convergence module tomodrgn.ctf module tomodrgn.dataset module tomodrgn.dose module tomodrgn.fft module tomodrgn.lattice module tomodrgn.lie_tools module tomodrgn.losses module tomodrgn.models module tomodrgn.mrc module tomodrgn.pose module tomodrgn.set_transformer module tomodrgn.so3_grid module tomodrgn.starfile module tomodrgn.utils module TomoParticlesMRCData (class in tomodrgn.dataset) TomoParticlesStarfile (class in tomodrgn.starfile) TomoParticlesStarfileStarHeaders (class in tomodrgn.starfile) total_header_bytes (MRCHeader property) train() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) train_batch() (in module tomodrgn.commands.train_nn) (in module tomodrgn.commands.train_vae) translate_ft() (Lattice method) translate_ht() (Lattice method) type() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) U unwrapped_state_dict() (DataParallelPassthrough method) update_apix() (MRCHeader method) update_origin() (MRCHeader method) V validate_particles_for_rendering() (in module tomodrgn.commands.subtomo2chimerax) validate_starfile() (in module tomodrgn.commands.subtomo2chimerax) validate_volume_mode_arguments() (in module tomodrgn.commands.subtomo2chimerax) vlog() (in module tomodrgn.utils) VolumeGenerator (class in tomodrgn.models) W warnexists() (in module tomodrgn.commands.downsample) window_mask() (in module tomodrgn.dataset) write() (GenericStarfile method) (in module tomodrgn.mrc) (MRCHeader method) (TiltSeriesStarfile method) (TomoParticlesStarfile method) write_downsampled_starfile() (in module tomodrgn.commands.downsample) write_labels_rgba_by_model() (in module tomodrgn.commands.subtomo2chimerax) write_mapback_script() (in module tomodrgn.commands.subtomo2chimerax) X xpu() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) xrot() (in module tomodrgn.utils) Y yrot() (in module tomodrgn.utils) Z zero_grad() (DataParallelPassthrough method) (EquivarianceLoss method) (FTPositionalDecoder method) (MAB method) (MedianPool1d method) (PMA method) (PoseTracker method) (ResidLinear method) (ResidLinearMLP method) (SAB method) (SetTransformer method) (TiltSeriesEncoder method) (TiltSeriesHetOnlyVAE method) zero_sphere() (in module tomodrgn.utils)