CLAUDE.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
cryoPARES/__init__.py
cryoPARES/cacheManager.py
cryoPARES/cli.py
cryoPARES/constants.py
cryoPARES.egg-info/PKG-INFO
cryoPARES.egg-info/SOURCES.txt
cryoPARES.egg-info/dependency_links.txt
cryoPARES.egg-info/entry_points.txt
cryoPARES.egg-info/requires.txt
cryoPARES.egg-info/top_level.txt
cryoPARES/configManager/__init__.py
cryoPARES/configs/__init__.py
cryoPARES/configs/mainConfig.py
cryoPARES/configs/datamanager_config/__init__.py
cryoPARES/configs/datamanager_config/augmentations_config.py
cryoPARES/configs/datamanager_config/datamanager_config.py
cryoPARES/configs/datamanager_config/particlesDataset_config.py
cryoPARES/configs/inference_config/__init__.py
cryoPARES/configs/inference_config/inference_config.py
cryoPARES/configs/inference_config/nnetInference_config.py
cryoPARES/configs/models_config/__init__.py
cryoPARES/configs/models_config/models_config.py
cryoPARES/configs/models_config/directionalnormalizer_config/__init__.py
cryoPARES/configs/models_config/directionalnormalizer_config/directionalnormalizer_config.py
cryoPARES/configs/models_config/image2sphere_config/__init__.py
cryoPARES/configs/models_config/image2sphere_config/gaussianFilters_config.py
cryoPARES/configs/models_config/image2sphere_config/image2sphere_config.py
cryoPARES/configs/models_config/image2sphere_config/so3Components_config.py
cryoPARES/configs/models_config/image2sphere_config/imageEncoder_config/__init__.py
cryoPARES/configs/models_config/image2sphere_config/imageEncoder_config/convMixer_config.py
cryoPARES/configs/models_config/image2sphere_config/imageEncoder_config/imageEncoder_config.py
cryoPARES/configs/models_config/image2sphere_config/imageEncoder_config/resNet_config.py
cryoPARES/configs/models_config/image2sphere_config/imageEncoder_config/unet_config.py
cryoPARES/configs/projmatching_config/__init__.py
cryoPARES/configs/projmatching_config/projmatching_config.py
cryoPARES/configs/reconstruct_config/__init__.py
cryoPARES/configs/reconstruct_config/reconstruct_config.py
cryoPARES/configs/train_config/__init__.py
cryoPARES/configs/train_config/train_config.py
cryoPARES/datamanager/__init__.py
cryoPARES/datamanager/augmentations.py
cryoPARES/datamanager/datamanager.py
cryoPARES/datamanager/particlesDataset.py
cryoPARES/datamanager/rawParticlesDataset.py
cryoPARES/datamanager/relionStarDataset.py
cryoPARES/datamanager/ctf/__init__.py
cryoPARES/datamanager/ctf/_test.py
cryoPARES/datamanager/ctf/common.py
cryoPARES/datamanager/ctf/fft_ctf.py
cryoPARES/datamanager/ctf/rfft_ctf.py
cryoPARES/experimental/__init__.py
cryoPARES/experimental/_rotateWigners.py
cryoPARES/experimental/escnn_groups_and_irreps.py
cryoPARES/experimental/rotateWigners.py
cryoPARES/geometry/__init__.py
cryoPARES/geometry/convert_angles.py
cryoPARES/geometry/grids.py
cryoPARES/geometry/metrics_angles.py
cryoPARES/geometry/nearest_neigs_sphere.py
cryoPARES/geometry/symmetry.py
cryoPARES/geometry/utilsGrid.py
cryoPARES/inference/__init__.py
cryoPARES/inference/infer.py
cryoPARES/inference/inferencer.py
cryoPARES/inference/daemon/__init__.py
cryoPARES/inference/daemon/_test_pickleFiller.py
cryoPARES/inference/daemon/daemonInference.py
cryoPARES/inference/daemon/materializePartialResults.py
cryoPARES/inference/daemon/queueManager.py
cryoPARES/inference/daemon/spoolingFiller.py
cryoPARES/inference/nnetWorkers/__init__.py
cryoPARES/inference/nnetWorkers/inferenceModel.py
cryoPARES/inference/nnetWorkers/tensorDataBuffer.py
cryoPARES/models/__init__.py
cryoPARES/models/model.py
cryoPARES/models/directionalNormalizer/__init__.py
cryoPARES/models/directionalNormalizer/directionalNormalizer.py
cryoPARES/models/image2sphere/__init__.py
cryoPARES/models/image2sphere/gaussianFilters.py
cryoPARES/models/image2sphere/image2sphere.py
cryoPARES/models/image2sphere/so3Components.py
cryoPARES/models/image2sphere/imageEncoder/__init__.py
cryoPARES/models/image2sphere/imageEncoder/_monai_unet.py
cryoPARES/models/image2sphere/imageEncoder/convMixer.py
cryoPARES/models/image2sphere/imageEncoder/imageEncoder.py
cryoPARES/models/image2sphere/imageEncoder/resNet.py
cryoPARES/models/image2sphere/imageEncoder/unet.py
cryoPARES/postprocessing/__init__.py
cryoPARES/postprocessing/fsc_utils.py
cryoPARES/postprocessing/guinier.py
cryoPARES/postprocessing/mask_utils.py
cryoPARES/postprocessing/postprocess.py
cryoPARES/postprocessing/sharpening.py
cryoPARES/postprocessing/methods/__init__.py
cryoPARES/postprocessing/methods/base.py
cryoPARES/postprocessing/methods/standard_bfactor.py
cryoPARES/projmatching/__init__.py
cryoPARES/projmatching/projMatcher.py
cryoPARES/projmatching/projmatching.py
cryoPARES/projmatching/projmatchingUtils/__init__.py
cryoPARES/projmatching/projmatchingUtils/extract_central_slices_as_real.py
cryoPARES/projmatching/projmatchingUtils/filterToResolution.py
cryoPARES/projmatching/projmatchingUtils/fourierOperations.py
cryoPARES/projmatching/projmatchingUtils/loggers.py
cryoPARES/projmatching/projmatchingUtils/myProgressBar.py
cryoPARES/reconstruction/__init__.py
cryoPARES/reconstruction/insert_central_slices_rfft_3d.py
cryoPARES/reconstruction/reconstruct.py
cryoPARES/reconstruction/reconstructor.py
cryoPARES/scripts/__init__.py
cryoPARES/scripts/compactify_checkpoint.py
cryoPARES/scripts/compare_poses.py
cryoPARES/scripts/computeFsc.py
cryoPARES/scripts/consensus_alignment.py
cryoPARES/scripts/consensus_picking.py
cryoPARES/scripts/gmm_hists.py
cryoPARES/scripts/hists_from_starfile.py
cryoPARES/scripts/manageStarfile.py
cryoPARES/scripts/plot_learning_curve.py
cryoPARES/scripts/regroup_starfile.py
cryoPARES/scripts/utils/create_noise_images.py
cryoPARES/scripts/utils/pred_calibration_estimation.py
cryoPARES/scripts/utils/randomize_particle_params.py
cryoPARES/scripts/utils/simulate_pref_orient.py
cryoPARES/simulation/__init__.py
cryoPARES/simulation/generateRandomStar.py
cryoPARES/simulation/simulateParticles.py
cryoPARES/simulation/simulateParticlesHelper.py
cryoPARES/train/__init__.py
cryoPARES/train/runTrainOnePartition.py
cryoPARES/train/train.py
cryoPARES/utils/__init__.py
cryoPARES/utils/checkpointReader.py
cryoPARES/utils/checkpointUtils.py
cryoPARES/utils/errorFormatting.py
cryoPARES/utils/paths.py
cryoPARES/utils/plUtils.py
cryoPARES/utils/reconstructionUtils.py
cryoPARES/utils/reproducibility.py
cryoPARES/utils/subprocessUtils.py
cryoPARES/utils/systemUtils.py
cryoPARES/utils/torchUtils.py
cryoPARES/utils/torch_fourier_shift_compat.py
cryoPARES/utils/torch_fourier_slice_compat.py
cryoPARES/utils/torch_grid_utils_compat.py
cryoPARES/utils/torch_image_interpolation_compat.py
tests/test_buffer_pool_fatal_error.py
tests/test_cacheManager.py
tests/test_cli_warnings.py
tests/test_configParser.py
tests/test_consensus_alignment.py
tests/test_daemon.py
tests/test_errorFormatting.py
tests/test_error_integration.py
tests/test_inference_distrib.py
tests/test_projmatching_distrib.py
tests/test_reconstruct_confidence.py
tests/test_reconstruct_distrib.py
tests/test_simclr_loss.py
tests/test_simulate_particles.py
tests/test_skip_localrefinement_scores.py
tests/test_so3_interpolation.py
tests/test_subprocessUtils.py
tests/test_tensorDataBuffer.py
tests/test_train_checkpoint_defaults.py