.flake8
.gitignore
.pre-commit-config.yaml
LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
sweep.sh
.github/CODEOWNERS
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/beta_release.yml
.github/workflows/docs.yml
.github/workflows/release.yml
.github/workflows/style.yml
.github/workflows/tests.yml
analysis_scripts/kmeans.py
analysis_scripts/plot_loss.py
analysis_scripts/plot_z1.py
analysis_scripts/plot_z2.py
analysis_scripts/plot_z_pca.py
analysis_scripts/run_umap.py
analysis_scripts/tsne.py
cryodrgn/__init__.py
cryodrgn/_version.py
cryodrgn/analysis.py
cryodrgn/beta_schedule.py
cryodrgn/command_line.py
cryodrgn/config.py
cryodrgn/ctf.py
cryodrgn/dataset.py
cryodrgn/fft.py
cryodrgn/healpy_grid.json
cryodrgn/lattice.py
cryodrgn/lie_tools.py
cryodrgn/losses.py
cryodrgn/make_healpy.py
cryodrgn/masking.py
cryodrgn/models.py
cryodrgn/mrcfile.py
cryodrgn/pose.py
cryodrgn/pose_search.py
cryodrgn/shift_grid.py
cryodrgn/shift_grid3.py
cryodrgn/so3_grid.py
cryodrgn/source.py
cryodrgn/starfile.py
cryodrgn/utils.py
cryodrgn.egg-info/PKG-INFO
cryodrgn.egg-info/SOURCES.txt
cryodrgn.egg-info/dependency_links.txt
cryodrgn.egg-info/entry_points.txt
cryodrgn.egg-info/not-zip-safe
cryodrgn.egg-info/requires.txt
cryodrgn.egg-info/top_level.txt
cryodrgn/commands/README.md
cryodrgn/commands/__init__.py
cryodrgn/commands/abinit_het.py
cryodrgn/commands/abinit_homo.py
cryodrgn/commands/analyze.py
cryodrgn/commands/analyze_landscape.py
cryodrgn/commands/analyze_landscape_full.py
cryodrgn/commands/backproject_voxel.py
cryodrgn/commands/direct_traversal.py
cryodrgn/commands/downsample.py
cryodrgn/commands/eval_images.py
cryodrgn/commands/eval_vol.py
cryodrgn/commands/filter.py
cryodrgn/commands/graph_traversal.py
cryodrgn/commands/parse_ctf_csparc.py
cryodrgn/commands/parse_ctf_star.py
cryodrgn/commands/parse_pose_csparc.py
cryodrgn/commands/parse_pose_star.py
cryodrgn/commands/pc_traversal.py
cryodrgn/commands/train_nn.py
cryodrgn/commands/train_vae.py
cryodrgn/commands/view_config.py
cryodrgn/commands_utils/README.md
cryodrgn/commands_utils/__init__.py
cryodrgn/commands_utils/add_psize.py
cryodrgn/commands_utils/clean.py
cryodrgn/commands_utils/concat_pkls.py
cryodrgn/commands_utils/filter_cs.py
cryodrgn/commands_utils/filter_mrcs.py
cryodrgn/commands_utils/filter_pkl.py
cryodrgn/commands_utils/filter_star.py
cryodrgn/commands_utils/flip_hand.py
cryodrgn/commands_utils/fsc.py
cryodrgn/commands_utils/gen_mask.py
cryodrgn/commands_utils/invert_contrast.py
cryodrgn/commands_utils/phase_flip.py
cryodrgn/commands_utils/plot_classes.py
cryodrgn/commands_utils/plot_fsc.py
cryodrgn/commands_utils/select_clusters.py
cryodrgn/commands_utils/select_random.py
cryodrgn/commands_utils/translate_mrcs.py
cryodrgn/commands_utils/view_cs_header.py
cryodrgn/commands_utils/view_header.py
cryodrgn/commands_utils/view_mrcs.py
cryodrgn/commands_utils/write_cs.py
cryodrgn/commands_utils/write_star.py
cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb
cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb
cryodrgn/templates/cryoDRGN_figures_template.ipynb
cryodrgn/templates/cryoDRGN_filtering_template.ipynb
cryodrgn/templates/cryoDRGN_viz_template.ipynb
docs/Makefile
docs/api.rst
docs/conf.py
docs/index.rst
docs/make.bat
docs/pages/cryodrgn2.md
docs/pages/empiar_tutorial.md
docs/pages/faq.md
docs/pages/installation.md
docs/pages/intro.md
docs/pages/landscape_analysis.md
docs/pages/large_datasets.md
docs/pages/assets/Untitled.png
docs/pages/assets/Untitled_1.png
docs/pages/assets/Untitled_10.png
docs/pages/assets/Untitled_11.png
docs/pages/assets/Untitled_12.png
docs/pages/assets/Untitled_13.png
docs/pages/assets/Untitled_14.png
docs/pages/assets/Untitled_15.png
docs/pages/assets/Untitled_16.png
docs/pages/assets/Untitled_17.png
docs/pages/assets/Untitled_18.png
docs/pages/assets/Untitled_19.png
docs/pages/assets/Untitled_2.png
docs/pages/assets/Untitled_20.png
docs/pages/assets/Untitled_21.png
docs/pages/assets/Untitled_22.png
docs/pages/assets/Untitled_23.png
docs/pages/assets/Untitled_24.png
docs/pages/assets/Untitled_25.png
docs/pages/assets/Untitled_26.png
docs/pages/assets/Untitled_27.png
docs/pages/assets/Untitled_28.png
docs/pages/assets/Untitled_29.png
docs/pages/assets/Untitled_3.png
docs/pages/assets/Untitled_30.png
docs/pages/assets/Untitled_31.png
docs/pages/assets/Untitled_32.png
docs/pages/assets/Untitled_33.png
docs/pages/assets/Untitled_34.png
docs/pages/assets/Untitled_35.png
docs/pages/assets/Untitled_36.png
docs/pages/assets/Untitled_37.png
docs/pages/assets/Untitled_38.png
docs/pages/assets/Untitled_39.png
docs/pages/assets/Untitled_4.png
docs/pages/assets/Untitled_40.png
docs/pages/assets/Untitled_41.png
docs/pages/assets/Untitled_42.png
docs/pages/assets/Untitled_43.png
docs/pages/assets/Untitled_44.png
docs/pages/assets/Untitled_45.png
docs/pages/assets/Untitled_46.png
docs/pages/assets/Untitled_47.png
docs/pages/assets/Untitled_48.png
docs/pages/assets/Untitled_49.png
docs/pages/assets/Untitled_5.png
docs/pages/assets/Untitled_50.png
docs/pages/assets/Untitled_51.png
docs/pages/assets/Untitled_52.png
docs/pages/assets/Untitled_53.png
docs/pages/assets/Untitled_54.png
docs/pages/assets/Untitled_55.png
docs/pages/assets/Untitled_56.png
docs/pages/assets/Untitled_57.png
docs/pages/assets/Untitled_58.png
docs/pages/assets/Untitled_59.png
docs/pages/assets/Untitled_6.png
docs/pages/assets/Untitled_60.png
docs/pages/assets/Untitled_61.png
docs/pages/assets/Untitled_62.png
docs/pages/assets/Untitled_63.png
docs/pages/assets/Untitled_64.png
docs/pages/assets/Untitled_65.png
docs/pages/assets/Untitled_66.png
docs/pages/assets/Untitled_67.png
docs/pages/assets/Untitled_68.png
docs/pages/assets/Untitled_7.png
docs/pages/assets/Untitled_8.png
docs/pages/assets/Untitled_9.png
docs/pages/assets/landscape_analysis_clustering_results1.png
docs/pages/assets/landscape_analysis_clustering_results2.png
docs/pages/assets/landscape_analysis_clustering_results3.png
docs/pages/assets/landscape_analysis_feature_space.png
docs/pages/assets/landscape_analysis_latent_space.png
docs/pages/assets/landscape_analysis_overview.png
docs/pages/assets/landscape_analysis_user_defined_mask.png
docs/pages/assets/preprocess1.png
docs/pages/assets/preprocess2.png
testing/diff_cryodrgn_pkl.py
testing/test_abinit.sh
testing/test_entropy.py
testing/test_pose_search_rag12_128.py
testing/test_pose_search_real_128.py
testing/test_pose_search_syn_64.py
testing/test_sta.sh
testing/test_translate.py
tests/conftest.py
tests/quicktest.sh
tests/test_add_psize.py
tests/test_backprojection.py
tests/test_clean.py
tests/test_dataset.py
tests/test_direct_traversal.py
tests/test_downsample.py
tests/test_entropy.py
tests/test_eval_images.py
tests/test_fft.py
tests/test_filter_mrcs.py
tests/test_filter_pkl.py
tests/test_flip_hand.py
tests/test_fsc.py
tests/test_graph_traversal.py
tests/test_integration.py
tests/test_invert_contrast.py
tests/test_masks.py
tests/test_mrc.py
tests/test_parse.py
tests/test_pc_traversal.py
tests/test_phase_flip.py
tests/test_read_filter_write.py
tests/test_reconstruct.py
tests/test_relion31.py
tests/test_select_clusters.py
tests/test_select_random.py
tests/test_source.py
tests/test_translate.py
tests/test_utils.py
tests/test_view_cs_header.py
tests/test_view_header.py
tests/test_view_mrcs.py
tests/test_writestar.py
tests/unittest.sh
tests/data/50S-vol.mrc
tests/data/FinalRefinement-OriginalParticles-PfCRT.star
tests/data/ay19102021_L3_position6_ribo_it09_bin8_1.82A.mrcs
tests/data/cryosparc_J2_particles_exported.cs
tests/data/cryosparc_P12_J24_001_particles.cs
tests/data/ctf1.pkl
tests/data/ctf2.pkl
tests/data/empiar_10076_7.cs
tests/data/empiar_10076_7.mrc
tests/data/empiar_10076_7.star
tests/data/hand-vol.mrc
tests/data/hand.5.mrcs
tests/data/hand.mrcs
tests/data/hand_11_particles.npy
tests/data/hand_rot.pkl
tests/data/hand_rot_trans.pkl
tests/data/hand_tilt.mrcs
tests/data/het_config.pkl
tests/data/het_weights.pkl
tests/data/im_shifted.npy
tests/data/ind100-rand.pkl
tests/data/ind100.pkl
tests/data/ind4.pkl
tests/data/ind5.pkl
tests/data/ind_39_sta_testing_bin8.pkl
tests/data/pose.cs.pkl
tests/data/pose.star.pkl
tests/data/relion31.6opticsgroups.star
tests/data/relion31.mrcs
tests/data/relion31.star
tests/data/relion31.v2.star
tests/data/spike-vol.mrc
tests/data/sta_ctf.pkl
tests/data/sta_pose.pkl
tests/data/sta_testing.star
tests/data/sta_testing_bin8.star
tests/data/test_ctf.100.pkl
tests/data/test_ctf.pkl
tests/data/toy.star
tests/data/toy_angles.pkl
tests/data/toy_projections.mrc
tests/data/toy_projections.mrcs
tests/data/toy_projections.star
tests/data/toy_projections.txt
tests/data/toy_projections_0-999.mrcs
tests/data/toy_projections_13.star
tests/data/toy_projections_2.txt
tests/data/toy_projections_dir.star
tests/data/toy_rot_trans.pkl
tests/data/toy_rot_zerotrans.pkl
tests/data/toy_trans.pkl
tests/data/toy_trans.zero.pkl
tests/data/toymodel_small_nocenter.mrc
tests/data/zvals_het-2_1k.pkl
tests/data/zvals_het-8_4k.pkl
tests/data/toy_datadir/toy_images_a.mrcs
tests/data/toy_datadir/toy_images_b.mrcs
utils/analyze_convergence.py