├── .github └── ISSUE_TEMPLATE │ └── bug_report.md ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── __init__.py ├── analysis_scripts ├── __main__.py ├── analyze.sh ├── convert_pytom.py ├── convert_star.py ├── convert_warp.py ├── eval_vol.sh ├── fsc.py ├── kmeans.py ├── parse_pose.sh ├── plot_loss.py ├── plot_z1.py ├── plot_z2.py ├── plot_z_pca.py ├── plotfsc.py ├── prepare.sh ├── prepare_multi.sh ├── run_umap.py ├── star2csv.py ├── tsne.py ├── union_star.py └── wrapper.py ├── cryodrgn ├── __init__.py ├── __main__.py ├── analysis.py ├── beta_schedule.py ├── commands │ ├── __init__.py │ ├── analyze.py │ ├── backproject_voxel.py │ ├── downsample.py │ ├── eval_images.py │ ├── eval_vol.py │ ├── graph_traversal.py │ ├── parse_ctf_csparc.py │ ├── parse_ctf_star.py │ ├── parse_multi_pose_star.py │ ├── parse_pose_csparc.py │ ├── parse_pose_star.py │ ├── pc_traversal.py │ ├── prepare_subtomos.py │ ├── preprocess.py │ ├── train_ad.py │ ├── train_aug.py │ ├── train_cv.py │ ├── train_fixed.py │ ├── train_multi.py │ ├── train_nn.py │ ├── train_ref.py │ ├── train_tomo.py │ ├── train_tomo_hvd.py │ ├── train_vae.py │ └── view_config.py ├── config.py ├── ctf.py ├── dataset.py ├── decoders.py ├── fft.py ├── group_stat.py ├── healpix_sampler.py ├── lattice.py ├── lie_tools.py ├── losses.py ├── models.py ├── mrc.py ├── pose.py ├── pose_encoder.py ├── shift_grid.py ├── shift_grid3.py ├── so3_grid.py ├── starfile.py ├── symm_data.json ├── symm_groups.py ├── symm_op.py ├── symm_ops.json ├── templates │ ├── cryoDRGN_filtering_template.ipynb │ └── cryoDRGN_viz_template.ipynb ├── test_group.py └── utils.py ├── environment.yml ├── environmentcu11.yml ├── environmentcu11torch11.yml ├── example ├── ._.DS_Store ├── ._decoder.png ├── ._encoder.png ├── ._hrd.png ├── ._hrds.png ├── ._riborna.png ├── ._riborotation.png ├── ._umap-bold.png ├── ._workflow.png ├── decoder.png ├── encoder.png ├── hrd.png ├── hrd2d.png ├── hrds.png ├── ribo │ └── ._.DS_Store ├── riborna.png ├── riborotation.png ├── umap-bold.png ├── umap-trpv.png ├── umaph15.png ├── umapht.png ├── umapr.png └── workflow.png ├── reconstruct_subtomo.py ├── relion_ctf_prepare.py ├── requirements.txt ├── setup.py ├── spec-file ├── testing ├── data │ ├── FinalRefinement-OriginalParticles-PfCRT.star │ ├── cryosparc_P12_J24_001_particles.cs │ ├── ctf1.pkl │ ├── ctf2.pkl │ ├── hand.5.mrcs │ ├── hand.mrcs │ ├── hand_rot.pkl │ ├── hand_tilt.mrcs │ ├── ind100.pkl │ ├── pose.cs.pkl │ ├── pose.star.pkl │ ├── relion31.mrcs │ ├── relion31.star │ ├── relion31.v2.star │ ├── toy.star │ ├── toy_angles.pkl │ ├── toy_projections.mrcs │ ├── toy_projections.star │ ├── toy_projections.txt │ ├── toy_rot_trans.pkl │ ├── toy_rot_zerotrans.pkl │ ├── toy_trans.pkl │ ├── toy_trans.zero.pkl │ └── toymodel_small_nocenter.mrc ├── quicktest.sh ├── test_entropy.py ├── test_mrc.py ├── test_parse.sh ├── test_relion31.sh ├── test_translate.py ├── test_utils.py ├── test_utils.sh └── unittest.sh └── utils ├── add_psize.py ├── 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