.gitignore
LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
versions.txt
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/docs.yml
.github/workflows/main.yml
analysis_scripts/fsc.py
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/plotfsc.py
analysis_scripts/run_umap.py
analysis_scripts/tsne.py
cryodrgn/__init__.py
cryodrgn/__main__.py
cryodrgn/_version.py
cryodrgn/analysis.py
cryodrgn/beta_schedule.py
cryodrgn/config.py
cryodrgn/ctf.py
cryodrgn/dataset.py
cryodrgn/fft.py
cryodrgn/lattice.py
cryodrgn/lie_tools.py
cryodrgn/losses.py
cryodrgn/models.py
cryodrgn/mrc.py
cryodrgn/pose.py
cryodrgn/shift_grid.py
cryodrgn/shift_grid3.py
cryodrgn/so3_grid.py
cryodrgn/starfile.py
cryodrgn/utils.py
cryodrgn/utils_exec.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/__init__.py
cryodrgn/commands/analyze.py
cryodrgn/commands/analyze_landscape.py
cryodrgn/commands/analyze_landscape_full.py
cryodrgn/commands/backproject_voxel.py
cryodrgn/commands/downsample.py
cryodrgn/commands/eval_images.py
cryodrgn/commands/eval_vol.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/preprocess.py
cryodrgn/commands/train_nn.py
cryodrgn/commands/train_vae.py
cryodrgn/commands/view_config.py
cryodrgn/commands_utils/__init__.py
cryodrgn/commands_utils/add_psize.py
cryodrgn/commands_utils/concat_pkls.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/invert_contrast.py
cryodrgn/commands_utils/phase_flip.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_star.py
cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb
cryodrgn/templates/cryoDRGN_filtering_template.ipynb
cryodrgn/templates/cryoDRGN_viz_template.ipynb
docs/Makefile
docs/conf.py
docs/index.rst
docs/make.bat
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
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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/quicktest.sh
testing/test_entropy.py
testing/test_mrc.py
testing/test_parse.sh
testing/test_relion31.sh
testing/test_translate.py
testing/test_utils.py
testing/test_utils.sh
testing/unittest.sh
testing/data/FinalRefinement-OriginalParticles-PfCRT.star
testing/data/cryosparc_P12_J24_001_particles.cs
testing/data/ctf1.pkl
testing/data/ctf2.pkl
testing/data/hand.5.mrcs
testing/data/hand.mrcs
testing/data/hand_rot.pkl
testing/data/hand_tilt.mrcs
testing/data/im_shifted.npy
testing/data/ind100.pkl
testing/data/ind3.pkl
testing/data/pose.cs.pkl
testing/data/pose.star.pkl
testing/data/relion31.mrcs
testing/data/relion31.star
testing/data/relion31.v2.star
testing/data/toy.star
testing/data/toy_angles.pkl
testing/data/toy_projections.mrcs
testing/data/toy_projections.star
testing/data/toy_projections.txt
testing/data/toy_rot_trans.pkl
testing/data/toy_rot_zerotrans.pkl
testing/data/toy_trans.pkl
testing/data/toy_trans.zero.pkl
testing/data/toymodel_small_nocenter.mrc
tests/test_entropy.py
tests/test_mrc.py
tests/test_parse.py
tests/test_pipeline.py
tests/test_quick.py
tests/test_relion31.py
tests/test_translate.py
tests/test_utils.py
tests/test_writestarfile.py
utils/analyze_convergence.py