Index

_

__init__() (cryoPARES.datamanager.augmentations.Augmenter method) (cryoPARES.datamanager.augmentations.Scheduler method) (cryoPARES.datamanager.datamanager.DataManager method) (cryoPARES.datamanager.datamanager.MultiInstanceSampler method) (cryoPARES.datamanager.particlesDataset.ParticlesDataset method) (cryoPARES.inference.daemon.daemonInference.DaemonInferencer method) (cryoPARES.inference.inferencer.SingleInferencer method), [1] (cryoPARES.models.directionalNormalizer.directionalNormalizer.DirectionalPercentileNormalizer method) (cryoPARES.models.image2sphere.image2sphere.Image2Sphere method) (cryoPARES.models.image2sphere.imageEncoder.convMixer.ConvMixer method) (cryoPARES.models.image2sphere.imageEncoder.convMixer.ResidualForConvMixer method) (cryoPARES.models.image2sphere.imageEncoder.resNet.ResNet method) (cryoPARES.models.image2sphere.imageEncoder.unet.ConvolutionalBlock method) (cryoPARES.models.image2sphere.imageEncoder.unet.Decoder method) (cryoPARES.models.image2sphere.imageEncoder.unet.DecodingBlock method) (cryoPARES.models.image2sphere.imageEncoder.unet.DecodingStage method) (cryoPARES.models.image2sphere.imageEncoder.unet.EncodingBlock method) (cryoPARES.models.image2sphere.imageEncoder.unet.MultiInputSequential method) (cryoPARES.models.image2sphere.imageEncoder.unet.Unet method) (cryoPARES.models.image2sphere.imageEncoder.unet.UnetEncoder method) (cryoPARES.models.model.PlModel method), [1] (cryoPARES.projmatching.projMatcher.ProjectionMatcher method), [1] (cryoPARES.reconstruction.reconstructor.ReconstructionParticlesDataset method) (cryoPARES.reconstruction.reconstructor.Reconstructor method), [1] (cryoPARES.train.runTrainOnePartition.TrainerPartition method) (cryoPARES.train.train.Trainer method), [1] (cryoPARES.utils.checkpointReader.CheckpointReader method)

__init_mixin__() (cryoPARES.models.model.RotationPredictionMixin method)

A

accelerator_selector() (in module cryoPARES.utils.torchUtils) add_if_not_none() (cryoPARES.models.image2sphere.imageEncoder.unet.ConvolutionalBlock static method) align_star() (cryoPARES.projmatching.projMatcher.ProjectionMatcher method), [1] (in module cryoPARES.projmatching.projMatcher) allow_zero_length_dataloader_with_multiple_devices (cryoPARES.datamanager.datamanager.DataManager attribute)

append() (cryoPARES.models.image2sphere.imageEncoder.unet.MultiInputSequential method) applyAugmentation() (cryoPARES.datamanager.augmentations.Augmenter method) (cryoPARES.datamanager.augmentations.AugmenterBase method) Augmenter (class in cryoPARES.datamanager.augmentations) augmenter (cryoPARES.datamanager.particlesDataset.ParticlesDataset property) AugmenterBase (class in cryoPARES.datamanager.augmentations)

B

backproject_particles() (cryoPARES.reconstruction.reconstructor.Reconstructor method), [1]

build_components() (cryoPARES.models.model.PlModel static method), [1]

C

cache (cryoPARES.models.image2sphere.image2sphere.Image2Sphere attribute) center_crop() (cryoPARES.models.image2sphere.imageEncoder.unet.DecodingBlock method) check_if_training_partion_done() (in module cryoPARES.train.runTrainOnePartition) CheckpointReader (class in cryoPARES.utils.checkpointReader) clean_reconstructer_buffers() (cryoPARES.inference.inferencer.SingleInferencer method), [1] close() (cryoPARES.utils.checkpointReader.CheckpointReader method) compute_ctf_rfft() (in module cryoPARES.datamanager.ctf.rfft_ctf) compute_probabilities() (cryoPARES.models.image2sphere.image2sphere.Image2Sphere method) configure_optimizers() (cryoPARES.models.model.PlModel method), [1] connect_to_queue() (in module cryoPARES.inference.daemon.queueManager) ConvMixer (class in cryoPARES.models.image2sphere.imageEncoder.convMixer) ConvolutionalBlock (class in cryoPARES.models.image2sphere.imageEncoder.unet) correct_ctf() (in module cryoPARES.datamanager.ctf.rfft_ctf) correlateF() (cryoPARES.projmatching.projMatcher.ProjectionMatcher method), [1] corrupt_with_ctf() (in module cryoPARES.datamanager.ctf.rfft_ctf) create_dataset() (cryoPARES.datamanager.datamanager.DataManager method) create_extraction_mask() (in module cryoPARES.models.image2sphere.image2sphere) create_shared_queue() (in module cryoPARES.inference.daemon.queueManager) create_shared_tensor() (in module cryoPARES.projmatching.projmatching) (in module cryoPARES.reconstruction.reconstruct) cryoPARES.datamanager.augmentations module cryoPARES.datamanager.ctf.rfft_ctf module cryoPARES.datamanager.datamanager module cryoPARES.datamanager.particlesDataset module cryoPARES.geometry.convert_angles module cryoPARES.geometry.grids module cryoPARES.geometry.metrics_angles module cryoPARES.geometry.symmetry module cryoPARES.inference.daemon.daemonInference module cryoPARES.inference.daemon.queueManager module

cryoPARES.inference.daemon.spoolingFiller module cryoPARES.inference.infer module cryoPARES.inference.inferencer module cryoPARES.models.directionalNormalizer.directionalNormalizer module cryoPARES.models.image2sphere.image2sphere module cryoPARES.models.image2sphere.imageEncoder.convMixer module cryoPARES.models.image2sphere.imageEncoder.resNet module cryoPARES.models.image2sphere.imageEncoder.unet module cryoPARES.models.model module cryoPARES.projmatching.projMatcher module cryoPARES.projmatching.projmatching module cryoPARES.reconstruction.reconstruct module cryoPARES.reconstruction.reconstructor module cryoPARES.train.runTrainOnePartition module cryoPARES.train.train module cryoPARES.utils.checkpointReader module cryoPARES.utils.checkpointUtils module cryoPARES.utils.paths module cryoPARES.utils.reconstructionUtils module cryoPARES.utils.torchUtils module

D

DaemonInferencer (class in cryoPARES.inference.daemon.daemonInference) data_to_numpy() (in module cryoPARES.utils.torchUtils) DataManager (class in cryoPARES.datamanager.datamanager) Decoder (class in cryoPARES.models.image2sphere.imageEncoder.unet)

DecodingBlock (class in cryoPARES.models.image2sphere.imageEncoder.unet) DecodingStage (class in cryoPARES.models.image2sphere.imageEncoder.unet) device (cryoPARES.projmatching.projMatcher.ProjectionMatcher property), [1] DirectionalPercentileNormalizer (class in cryoPARES.models.directionalNormalizer.directionalNormalizer) distributed_inference() (in module cryoPARES.inference.infer)

E

EncodingBlock (class in cryoPARES.models.image2sphere.imageEncoder.unet) euler_angles_to_matrix() (in module cryoPARES.geometry.convert_angles) execute_trainOnePartition() (in module cryoPARES.train.runTrainOnePartition)

exists() (cryoPARES.utils.checkpointReader.CheckpointReader method) extract_ccor_max() (in module cryoPARES.projmatching.projMatcher) extract_sh_coeffs_fast() (in module cryoPARES.models.image2sphere.image2sphere)

F

find_configs_root() (in module cryoPARES.utils.paths) find_last_version() (in module cryoPARES.utils.checkpointUtils) find_project_root() (in module cryoPARES.utils.paths) fit() (cryoPARES.models.directionalNormalizer.directionalNormalizer.DirectionalPercentileNormalizer method) fix_upsampling_type() (in module cryoPARES.models.image2sphere.imageEncoder.unet) forward() (cryoPARES.models.directionalNormalizer.directionalNormalizer.DirectionalPercentileNormalizer method) (cryoPARES.models.image2sphere.imageEncoder.convMixer.ConvMixer method) (cryoPARES.models.image2sphere.imageEncoder.convMixer.ResidualForConvMixer method) (cryoPARES.models.image2sphere.imageEncoder.resNet.ResNet method) (cryoPARES.models.image2sphere.imageEncoder.unet.ConvolutionalBlock method) (cryoPARES.models.image2sphere.imageEncoder.unet.Decoder method) (cryoPARES.models.image2sphere.imageEncoder.unet.DecodingBlock method) (cryoPARES.models.image2sphere.imageEncoder.unet.DecodingStage method) (cryoPARES.models.image2sphere.imageEncoder.unet.EncodingBlock method) (cryoPARES.models.image2sphere.imageEncoder.unet.MultiInputSequential method) (cryoPARES.models.image2sphere.imageEncoder.unet.Unet method) (cryoPARES.models.image2sphere.imageEncoder.unet.UnetEncoder method) (cryoPARES.models.model.PlModel method), [1] (cryoPARES.projmatching.projMatcher.ProjectionMatcher method), [1]

forward_and_loss() (cryoPARES.models.image2sphere.image2sphere.Image2Sphere method) forward_standard() (cryoPARES.models.image2sphere.image2sphere.Image2Sphere method) forward_with_neigs() (cryoPARES.models.image2sphere.image2sphere.Image2Sphere method) from_wignerD_to_topKMats() (cryoPARES.models.image2sphere.image2sphere.Image2Sphere method)

G

generate() (cryoPARES.datamanager.augmentations.Scheduler method) generate_volume() (cryoPARES.reconstruction.reconstructor.Reconstructor method), [1] get_all_available_items() (in module cryoPARES.inference.daemon.queueManager) get_best_checkpoint() (in module cryoPARES.utils.checkpointUtils) get_buffers() (cryoPARES.reconstruction.reconstructor.Reconstructor method), [1] get_continue_checkpoint_fname() (cryoPARES.train.train.Trainer method), [1] get_conv_transpose_layer() (in module cryoPARES.models.image2sphere.imageEncoder.unet) get_device() (cryoPARES.reconstruction.reconstructor.Reconstructor method), [1] get_done_fname() (in module cryoPARES.train.runTrainOnePartition) get_downsampling_layer() (in module cryoPARES.models.image2sphere.imageEncoder.unet) get_eulers() (in module cryoPARES.projmatching.projMatcher) get_example_random_batch() (in module cryoPARES.datamanager.datamanager)

get_finetune_checkpoint_fname() (cryoPARES.train.train.Trainer method), [1] get_most_recent_file() (in module cryoPARES.utils.paths) get_number_image_channels() (in module cryoPARES.datamanager.datamanager) get_real_path() (cryoPARES.utils.checkpointReader.CheckpointReader method) get_reconstructions_dir() (in module cryoPARES.train.runTrainOnePartition) get_rotmat() (in module cryoPARES.projmatching.projMatcher) (in module cryoPARES.utils.reconstructionUtils) get_sincsq() (cryoPARES.reconstruction.reconstructor.Reconstructor static method), [1] get_upsampling_layer() (in module cryoPARES.models.image2sphere.imageEncoder.unet) get_version_to_use() (in module cryoPARES.utils.checkpointUtils) get_vol() (in module cryoPARES.utils.reconstructionUtils) glob() (cryoPARES.utils.checkpointReader.CheckpointReader method)

H

hp_order_to_degs() (in module cryoPARES.geometry.grids)

I

identity() (cryoPARES.datamanager.augmentations.Scheduler method) Image2Sphere (class in cryoPARES.models.image2sphere.image2sphere)

increment_generic() (in module cryoPARES.utils.checkpointUtils) increment_version() (in module cryoPARES.utils.checkpointUtils)

L

linear_down() (cryoPARES.datamanager.augmentations.Scheduler method) linear_up() (cryoPARES.datamanager.augmentations.Scheduler method) load() (cryoPARES.models.directionalNormalizer.directionalNormalizer.DirectionalPercentileNormalizer class method)

load_jit() (cryoPARES.utils.checkpointReader.CheckpointReader method) load_ParticlesStarSet() (cryoPARES.datamanager.particlesDataset.ParticlesDataset method) load_torch() (cryoPARES.utils.checkpointReader.CheckpointReader method)

M

main() (in module cryoPARES.inference.daemon.queueManager) (in module cryoPARES.inference.daemon.spoolingFiller) (in module cryoPARES.inference.infer) (in module cryoPARES.projmatching.projmatching) (in module cryoPARES.reconstruction.reconstruct) (in module cryoPARES.train.train) matrix_to_euler_angles() (in module cryoPARES.geometry.convert_angles) max_resoluton_freq_pixels (cryoPARES.projmatching.projMatcher.ProjectionMatcher property), [1] mean_rot_matrix() (in module cryoPARES.geometry.metrics_angles) module cryoPARES.datamanager.augmentations cryoPARES.datamanager.ctf.rfft_ctf cryoPARES.datamanager.datamanager cryoPARES.datamanager.particlesDataset cryoPARES.geometry.convert_angles cryoPARES.geometry.grids cryoPARES.geometry.metrics_angles cryoPARES.geometry.symmetry cryoPARES.inference.daemon.daemonInference cryoPARES.inference.daemon.queueManager cryoPARES.inference.daemon.spoolingFiller cryoPARES.inference.infer cryoPARES.inference.inferencer cryoPARES.models.directionalNormalizer.directionalNormalizer cryoPARES.models.image2sphere.image2sphere cryoPARES.models.image2sphere.imageEncoder.convMixer cryoPARES.models.image2sphere.imageEncoder.resNet cryoPARES.models.image2sphere.imageEncoder.unet cryoPARES.models.model cryoPARES.projmatching.projMatcher cryoPARES.projmatching.projmatching cryoPARES.reconstruction.reconstruct cryoPARES.reconstruction.reconstructor cryoPARES.train.runTrainOnePartition cryoPARES.train.train cryoPARES.utils.checkpointReader cryoPARES.utils.checkpointUtils cryoPARES.utils.paths cryoPARES.utils.reconstructionUtils cryoPARES.utils.torchUtils

monitor_directory() (in module cryoPARES.inference.daemon.spoolingFiller) move_buffers_to_share_mem() (cryoPARES.reconstruction.reconstructor.Reconstructor method), [1] MultiInputSequential (class in cryoPARES.models.image2sphere.imageEncoder.unet) MultiInstanceSampler (class in cryoPARES.datamanager.datamanager)

N

nearest_rotmat_idx() (in module cryoPARES.geometry.metrics_angles)

nnet_image_size_px (cryoPARES.datamanager.particlesDataset.ParticlesDataset property)

O

on_train_end() (cryoPARES.models.model.PlModel method), [1] optimizer_step_v1() (cryoPARES.models.model.PlModel method), [1] optimizer_step_v2() (cryoPARES.models.model.PlModel method), [1]

original_image_size() (cryoPARES.datamanager.particlesDataset.ParticlesDataset method) original_sampling_rate() (cryoPARES.datamanager.particlesDataset.ParticlesDataset method) out_channels (cryoPARES.models.image2sphere.imageEncoder.unet.EncodingBlock property) (cryoPARES.models.image2sphere.imageEncoder.unet.UnetEncoder property)

P

particle_shape (cryoPARES.reconstruction.reconstructor.ReconstructionParticlesDataset property) particles (cryoPARES.datamanager.particlesDataset.ParticlesDataset property) (cryoPARES.reconstruction.reconstructor.ReconstructionParticlesDataset property) ParticlesDataset (class in cryoPARES.datamanager.particlesDataset) pick_hp_order() (in module cryoPARES.geometry.grids) PlModel (class in cryoPARES.models.model), [1] plot_so3_distribution() (in module cryoPARES.models.image2sphere.image2sphere)

predict_dataloader() (cryoPARES.datamanager.datamanager.DataManager method) predict_wignerDs() (cryoPARES.models.image2sphere.image2sphere.Image2Sphere method) prepare_data() (cryoPARES.datamanager.datamanager.DataManager method) prepare_data_per_node (cryoPARES.datamanager.datamanager.DataManager attribute) preprocess_particles() (cryoPARES.projmatching.projMatcher.ProjectionMatcher method), [1] ProjectionMatcher (class in cryoPARES.projmatching.projMatcher), [1] projmatching_starfile() (in module cryoPARES.projmatching.projmatching)

Q

queue_connection() (in module cryoPARES.inference.daemon.queueManager)

queue_manager_server() (in module cryoPARES.inference.daemon.queueManager) QueueManager (class in cryoPARES.inference.daemon.queueManager)

R

read_bytes() (cryoPARES.utils.checkpointReader.CheckpointReader method) read_text() (cryoPARES.utils.checkpointReader.CheckpointReader method) reconstruct_starfile() (in module cryoPARES.reconstruction.reconstruct) (in module cryoPARES.reconstruction.reconstructor) ReconstructionParticlesDataset (class in cryoPARES.reconstruction.reconstructor) Reconstructor (class in cryoPARES.reconstruction.reconstructor), [1] ResidualForConvMixer (class in cryoPARES.models.image2sphere.imageEncoder.convMixer) resize_and_padCrop_tensorBatch() (in module cryoPARES.datamanager.particlesDataset) resizeImage() (cryoPARES.datamanager.particlesDataset.ParticlesDataset method) ResNet (class in cryoPARES.models.image2sphere.imageEncoder.resNet) resolve_data() (cryoPARES.inference.daemon.daemonInference.DaemonInferencer method)

resolve_halfset_lists() (cryoPARES.inference.inferencer.SingleInferencer static method), [1] rotation_error_rads() (in module cryoPARES.geometry.metrics_angles) rotation_error_with_sym() (in module cryoPARES.geometry.metrics_angles) rotation_magnitude() (in module cryoPARES.geometry.metrics_angles) RotationPredictionMixin (class in cryoPARES.models.model) rotmats_to_cone_id() (cryoPARES.models.directionalNormalizer.directionalNormalizer.DirectionalPercentileNormalizer method) rotTransImage() (in module cryoPARES.datamanager.augmentations) run() (cryoPARES.inference.daemon.daemonInference.DaemonInferencer method) (cryoPARES.inference.inferencer.SingleInferencer method), [1] (cryoPARES.train.runTrainOnePartition.TrainerPartition method) (cryoPARES.train.train.Trainer method), [1]

S

sampling_rate (cryoPARES.datamanager.particlesDataset.ParticlesDataset property) (cryoPARES.reconstruction.reconstructor.ReconstructionParticlesDataset property) save() (cryoPARES.models.directionalNormalizer.directionalNormalizer.DirectionalPercentileNormalizer method) Scheduler (class in cryoPARES.datamanager.augmentations) set_metadata_from_particles() (cryoPARES.reconstruction.reconstructor.Reconstructor method), [1]

signal_handler() (in module cryoPARES.inference.daemon.queueManager) simCLR_like_loss() (cryoPARES.models.image2sphere.image2sphere.Image2Sphere method) SingleInferencer (class in cryoPARES.inference.inferencer), [1] so3_to_cone_ids() (cryoPARES.models.directionalNormalizer.directionalNormalizer.DirectionalPercentileNormalizer method) symmetry (cryoPARES.inference.inferencer.SingleInferencer property), [1] symmetry_group (cryoPARES.datamanager.particlesDataset.ParticlesDataset property)

T

test_custom_pattern_with_dir() (in module cryoPARES.utils.checkpointUtils) test_dataloader() (cryoPARES.datamanager.datamanager.DataManager method) test_find_last_version_directories() (in module cryoPARES.utils.checkpointUtils) test_find_last_version_empty() (in module cryoPARES.utils.checkpointUtils) test_find_last_version_files() (in module cryoPARES.utils.checkpointUtils) test_find_last_version_mixed() (in module cryoPARES.utils.checkpointUtils) test_get_version_to_use_custom_pattern_empty() (in module cryoPARES.utils.checkpointUtils) test_get_version_to_use_empty() (in module cryoPARES.utils.checkpointUtils)

test_get_version_to_use_existing_dir() (in module cryoPARES.utils.checkpointUtils) test_get_version_to_use_existing_file() (in module cryoPARES.utils.checkpointUtils) test_increment_version() (in module cryoPARES.utils.checkpointUtils) tmpdir() (in module cryoPARES.utils.checkpointUtils) train_dataloader() (cryoPARES.datamanager.datamanager.DataManager method) Trainer (class in cryoPARES.train.train), [1] TrainerPartition (class in cryoPARES.train.runTrainOnePartition) training_step() (cryoPARES.models.model.PlModel method), [1]

U

Unet (class in cryoPARES.models.image2sphere.imageEncoder.unet)

UnetEncoder (class in cryoPARES.models.image2sphere.imageEncoder.unet) updateMd() (cryoPARES.datamanager.particlesDataset.ParticlesDataset method)

V

val_dataloader() (cryoPARES.datamanager.datamanager.DataManager method)

validation_step() (cryoPARES.models.model.PlModel method), [1]

W

worker() (in module cryoPARES.inference.infer) (in module cryoPARES.projmatching.projmatching) (in module cryoPARES.reconstruction.reconstruct)

write_vol() (in module cryoPARES.utils.reconstructionUtils)

Z

zero_buffers() (cryoPARES.reconstruction.reconstructor.Reconstructor method), [1]