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tomoDRGN v1.0.1.dev3
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Overview
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Command Usage
API
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TomoDRGN core modules
tomodrgn.analysis
tomodrgn.analysis.cluster_gmm
tomodrgn.analysis.cluster_kmeans
tomodrgn.analysis.combine_ind
tomodrgn.analysis.convert_angstroms_to_voxels
tomodrgn.analysis.convert_original_indices
tomodrgn.analysis.get_colors_chimerax
tomodrgn.analysis.get_colors_matplotlib
tomodrgn.analysis.get_ind_for_cluster
tomodrgn.analysis.get_nearest_point
tomodrgn.analysis.get_pc_traj
tomodrgn.analysis.ipy_plot_interactive
tomodrgn.analysis.ipy_tomo_ptcl_viewer
tomodrgn.analysis.load_dataframe
tomodrgn.analysis.parse_all_losses
tomodrgn.analysis.parse_loss
tomodrgn.analysis.plot_by_cluster
tomodrgn.analysis.plot_by_cluster_subplot
tomodrgn.analysis.plot_euler
tomodrgn.analysis.plot_label_count_distribution
tomodrgn.analysis.plot_losses
tomodrgn.analysis.plot_projections
tomodrgn.analysis.plot_three_column_correlation
tomodrgn.analysis.plot_translations
tomodrgn.analysis.recursive_load_dataframe
tomodrgn.analysis.run_pca
tomodrgn.analysis.run_tsne
tomodrgn.analysis.run_umap
tomodrgn.analysis.scatter_annotate
tomodrgn.analysis.scatter_annotate_hex
tomodrgn.analysis.scatter_color
tomodrgn.beta_schedule
tomodrgn.beta_schedule.get_beta_schedule
tomodrgn.beta_schedule.ConstantSchedule
tomodrgn.beta_schedule.CyclicalSchedule
tomodrgn.beta_schedule.LinearSchedule
tomodrgn.config
tomodrgn.config.print_config
tomodrgn.config.save_config
tomodrgn.convergence
tomodrgn.convergence.calc_ccs_alltoall_intraepoch
tomodrgn.convergence.calc_ccs_alltogroundtruth
tomodrgn.convergence.calc_ccs_pairwise_epochs
tomodrgn.convergence.calc_fscs_pairwise_epochs
tomodrgn.convergence.calc_kld_two_gaussians
tomodrgn.convergence.calc_test_train_pair_volumes_cc_complement
tomodrgn.convergence.calc_test_train_pair_volumes_fscs
tomodrgn.convergence.encoder_latent_shifts
tomodrgn.convergence.follow_candidate_particles
tomodrgn.convergence.fsc_referencevol_to_manyvols
tomodrgn.convergence.generate_test_train_pair_volumes
tomodrgn.convergence.plot_latent_pca
tomodrgn.convergence.plot_latent_umap
tomodrgn.convergence.plot_loss
tomodrgn.convergence.sketch_via_umap_local_maxima
tomodrgn.ctf
tomodrgn.ctf.compute_ctf
tomodrgn.ctf.print_ctf_params
tomodrgn.dataset
tomodrgn.dataset.load_particles
tomodrgn.dataset.load_sta_dataset
tomodrgn.dataset.window_mask
tomodrgn.dataset.TiltSeriesMRCData
tomodrgn.dataset.TomoParticlesMRCData
tomodrgn.dose
tomodrgn.dose.calculate_critical_dose_per_frequency
tomodrgn.dose.calculate_dose_mask
tomodrgn.dose.calculate_dose_weights
tomodrgn.dose.calculate_spatial_frequencies
tomodrgn.dose.calculate_tilt_weights
tomodrgn.dose.combine_dose_tilt_weights
tomodrgn.dose.plot_weight_distribution
tomodrgn.fft
tomodrgn.fft.fft2_center
tomodrgn.fft.fft2_center_torch
tomodrgn.fft.fft3_center
tomodrgn.fft.fft3_center_torch
tomodrgn.fft.ht2_center
tomodrgn.fft.ht2_center_torch
tomodrgn.fft.ht3_center
tomodrgn.fft.ht3_center_torch
tomodrgn.fft.ifft2_center
tomodrgn.fft.ifft2_center_torch
tomodrgn.fft.ifft3_center
tomodrgn.fft.ifft3_center_torch
tomodrgn.fft.iht2_center
tomodrgn.fft.iht2_center_torch
tomodrgn.fft.iht3_center
tomodrgn.fft.iht3_center_torch
tomodrgn.fft.symmetrize_ht
tomodrgn.lattice
tomodrgn.lattice.EvenLattice
tomodrgn.lattice.Lattice
tomodrgn.lie_tools
tomodrgn.lie_tools.SO3_to_quaternions
tomodrgn.lie_tools.SO3_to_s2s2
tomodrgn.lie_tools.expmap
tomodrgn.lie_tools.logsumexp
tomodrgn.lie_tools.map_to_lie_algebra
tomodrgn.lie_tools.quaternions_to_SO3
tomodrgn.lie_tools.random_SO3
tomodrgn.lie_tools.random_quaternions
tomodrgn.lie_tools.s2s1rodrigues
tomodrgn.lie_tools.s2s2_to_SO3
tomodrgn.lie_tools.so3_entropy
tomodrgn.lie_tools.so3_entropy_old
tomodrgn.losses
tomodrgn.losses.EquivarianceLoss
tomodrgn.models
tomodrgn.models.mlp_ascii
tomodrgn.models.print_tiltserieshetonlyvae_ascii
tomodrgn.models.DataParallelPassthrough
tomodrgn.models.FTPositionalDecoder
tomodrgn.models.MedianPool1d
tomodrgn.models.ResidLinear
tomodrgn.models.ResidLinearMLP
tomodrgn.models.TiltSeriesEncoder
tomodrgn.models.TiltSeriesHetOnlyVAE
tomodrgn.models.VolumeGenerator
tomodrgn.mrc
tomodrgn.mrc.parse_header
tomodrgn.mrc.parse_mrc
tomodrgn.mrc.parse_mrc_list
tomodrgn.mrc.write
tomodrgn.mrc.LazyImage
tomodrgn.mrc.LazyImageStack
tomodrgn.mrc.MRCHeader
tomodrgn.pose
tomodrgn.pose.PoseTracker
tomodrgn.set_transformer
tomodrgn.set_transformer.MAB
tomodrgn.set_transformer.PMA
tomodrgn.set_transformer.SAB
tomodrgn.set_transformer.SetTransformer
tomodrgn.so3_grid
tomodrgn.so3_grid.base_SO3_grid
tomodrgn.so3_grid.get_base_ind
tomodrgn.so3_grid.get_neighbor
tomodrgn.so3_grid.get_s1_neighbor
tomodrgn.so3_grid.get_s2_neighbor
tomodrgn.so3_grid.grid_SO3
tomodrgn.so3_grid.grid_s1
tomodrgn.so3_grid.grid_s2
tomodrgn.so3_grid.hopf_to_quat
tomodrgn.starfile
tomodrgn.starfile.is_starfile_optimisation_set
tomodrgn.starfile.load_sta_starfile
tomodrgn.starfile.GenericStarfile
tomodrgn.starfile.TiltSeriesStarfile
tomodrgn.starfile.TiltSeriesStarfileStarHeaders
tomodrgn.starfile.TomoParticlesStarfile
tomodrgn.starfile.TomoParticlesStarfileStarHeaders
tomodrgn.utils
tomodrgn.utils.calc_cc
tomodrgn.utils.calc_fsc
tomodrgn.utils.calc_lowpass_filter_mask
tomodrgn.utils.calc_real_space_mask
tomodrgn.utils.check_git_revision_hash
tomodrgn.utils.check_memory_usage
tomodrgn.utils.first_n_factors
tomodrgn.utils.flog
tomodrgn.utils.get_default_device
tomodrgn.utils.get_latest_epoch
tomodrgn.utils.load_pkl
tomodrgn.utils.log
tomodrgn.utils.lowpass_filter
tomodrgn.utils.prefix_paths
tomodrgn.utils.print_progress_bar
tomodrgn.utils.rot_3d_from_eman
tomodrgn.utils.rot_3d_from_relion
tomodrgn.utils.rot_3d_from_relion_scipy
tomodrgn.utils.rot_3d_to_relion_scipy
tomodrgn.utils.save_pkl
tomodrgn.utils.vlog
tomodrgn.utils.xrot
tomodrgn.utils.yrot
tomodrgn.utils.zero_sphere
tomodrgn.utils.Memoized
TomoDRGN commands
tomodrgn.commands.analyze
tomodrgn.commands.analyze.add_args
tomodrgn.commands.analyze.analyze_z_multidimensional
tomodrgn.commands.analyze.analyze_z_onedimensional
tomodrgn.commands.analyze.main
tomodrgn.commands.analyze_volumes
tomodrgn.commands.analyze_volumes.add_args
tomodrgn.commands.analyze_volumes.main
tomodrgn.commands.analyze_volumes.make_plots
tomodrgn.commands.backproject_voxel
tomodrgn.commands.backproject_voxel.add_args
tomodrgn.commands.backproject_voxel.add_slice
tomodrgn.commands.backproject_voxel.backproject_dataset
tomodrgn.commands.backproject_voxel.main
tomodrgn.commands.backproject_voxel.save_map
tomodrgn.commands.cleanup
tomodrgn.commands.cleanup.add_args
tomodrgn.commands.cleanup.main
tomodrgn.commands.convergence_nn
tomodrgn.commands.convergence_nn.add_args
tomodrgn.commands.convergence_nn.main
tomodrgn.commands.convergence_nn.make_plots
tomodrgn.commands.convergence_vae
tomodrgn.commands.convergence_vae.add_args
tomodrgn.commands.convergence_vae.main
tomodrgn.commands.downsample
tomodrgn.commands.downsample.add_args
tomodrgn.commands.downsample.collate_particle_tilts
tomodrgn.commands.downsample.downsample_images
tomodrgn.commands.downsample.main
tomodrgn.commands.downsample.mkbasedir
tomodrgn.commands.downsample.warnexists
tomodrgn.commands.downsample.write_downsampled_starfile
tomodrgn.commands.downsample.ImageDataset
tomodrgn.commands.eval_images
tomodrgn.commands.eval_images.add_args
tomodrgn.commands.eval_images.main
tomodrgn.commands.eval_vol
tomodrgn.commands.eval_vol.add_args
tomodrgn.commands.eval_vol.main
tomodrgn.commands.filter_star
tomodrgn.commands.filter_star.add_args
tomodrgn.commands.filter_star.check_args_compatible
tomodrgn.commands.filter_star.filter_image_series_starfile
tomodrgn.commands.filter_star.filter_volume_series_starfile
tomodrgn.commands.filter_star.main
tomodrgn.commands.graph_traversal
tomodrgn.commands.graph_traversal.add_args
tomodrgn.commands.graph_traversal.main
tomodrgn.commands.graph_traversal.LatentGraph
tomodrgn.commands.pc_traversal
tomodrgn.commands.pc_traversal.add_args
tomodrgn.commands.pc_traversal.analyze_data_support
tomodrgn.commands.pc_traversal.main
tomodrgn.commands.subtomo2chimerax
tomodrgn.commands.subtomo2chimerax.add_args
tomodrgn.commands.subtomo2chimerax.generate_color_per_particle
tomodrgn.commands.subtomo2chimerax.main
tomodrgn.commands.subtomo2chimerax.validate_particles_for_rendering
tomodrgn.commands.subtomo2chimerax.validate_starfile
tomodrgn.commands.subtomo2chimerax.validate_volume_mode_arguments
tomodrgn.commands.subtomo2chimerax.write_labels_rgba_by_model
tomodrgn.commands.subtomo2chimerax.write_mapback_script
tomodrgn.commands.train_nn
tomodrgn.commands.train_nn.add_args
tomodrgn.commands.train_nn.decode_batch
tomodrgn.commands.train_nn.loss_function
tomodrgn.commands.train_nn.main
tomodrgn.commands.train_nn.save_checkpoint
tomodrgn.commands.train_nn.train_batch
tomodrgn.commands.train_vae
tomodrgn.commands.train_vae.add_args
tomodrgn.commands.train_vae.decode_batch
tomodrgn.commands.train_vae.encode_batch
tomodrgn.commands.train_vae.encoder_inference
tomodrgn.commands.train_vae.loss_function
tomodrgn.commands.train_vae.main
tomodrgn.commands.train_vae.preprocess_batch
tomodrgn.commands.train_vae.save_checkpoint
tomodrgn.commands.train_vae.train_batch
tomodrgn.commands.view_config
tomodrgn.commands.view_config.add_args
tomodrgn.commands.view_config.main
API Reference
tomodrgn.commands.backproject_voxel
tomodrgn.commands.backproject_voxel.main
tomodrgn.commands.backproject_voxel.main
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