Index

_

__init__() (BaseDataModule method) (BaseModel method) (CryoVIT method) (FileDataModule method) (FileDataset method) (FractionalSampleDataModule method) (MultiSampleDataModule method) (SAM2 method) (SingleSampleDataModule method) (TomoDataset method) (UNet3D method) (VITDataset method)

A

accelerator (BaseTrainer attribute)

additional_keys (BaseExperimentConfig attribute) aux_data (BatchedModelResult attribute)

B

BaseDataModule (class in cryovit.config) (class in cryovit.datamodules) BaseExperimentConfig (class in cryovit.config) BaseModel (class in cryovit.config) (class in cryovit.models)

BaseTrainer (class in cryovit.config) batch_size (DinoFeaturesConfig attribute) BatchedModelResult (class in cryovit.types) BatchedTomogramData (class in cryovit.types) BatchedTomogramMetadata (class in cryovit.types)

C

callbacks (BaseExperimentConfig attribute) ckpt_path (BaseExperimentConfig attribute) compile() (SAM2 method) configure_optimizers() (BaseModel method) (SAM2 method) create_sam_model_from_weights() (in module cryovit.models) CryoVIT (class in cryovit.models) cryovit.config module cryovit.datamodules module

cryovit.datasets module cryovit.models module cryovit.run module cryovit.types module cryovit.utils module csv_name (ExperimentPaths attribute) custom_kwargs (BaseModel attribute)

D

data (BatchedModelResult attribute) data_dir (ExperimentPaths attribute) dataloader (BaseDataModule attribute) datamodule (BaseExperimentConfig attribute) (DinoFeaturesConfig attribute) dataset (BaseDataModule attribute) default_root_dir (BaseTrainer attribute) device (BatchedTomogramData property) (BatchedTomogramMetadata property) (TomogramData property)

devices (BaseTrainer attribute) dino_dir (DinoFeaturesConfig attribute) dino_name (ExperimentPaths attribute) DinoFeaturesConfig (class in cryovit.config) drange (FileMetadata attribute) dshape (FileMetadata attribute) dtype (FileMetadata attribute) dumps() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method)

E

enable_checkpointing (BaseTrainer attribute) enable_model_summary (BaseTrainer attribute)

exp_dir (ExperimentPaths attribute) ExperimentPaths (class in cryovit.config) export_features (DinoFeaturesConfig attribute)

F

feature_name (ExperimentPaths attribute) fields() (BatchedTomogramData class method) (BatchedTomogramMetadata class method) (TomogramData class method) FileData (class in cryovit.types) FileDataModule (class in cryovit.datamodules) FileDataset (class in cryovit.datasets) FileMetadata (class in cryovit.utils) flat_tomo_batch (BatchedTomogramData property)

forward() (BaseModel method) (CryoVIT method) (SAM2 method) (UNet3D method) forward_volume() (UNet3D method) FractionalSampleDataModule (class in cryovit.datamodules) freeze_parameters() (SAM2 method) from_tensordict() (BatchedTomogramData class method) (BatchedTomogramMetadata class method) (TomogramData class method)

G

get() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method)

I

id_generator() (in module cryovit.utils)

index_to_flat_batch() (BatchedTomogramData method) input_key (BaseModel attribute)

L

label (BatchedModelResult attribute) label_key (BaseExperimentConfig attribute) (SavedModel attribute) label_path (FileData attribute) labels (FileData attribute) load() (BatchedTomogramData class method) (BatchedTomogramMetadata class method) (TomogramData class method) load_() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) load_data() (in module cryovit.utils) load_files_from_path() (in module cryovit.utils) load_labels() (in module cryovit.utils)

load_memmap() (BatchedTomogramData class method) (BatchedTomogramMetadata class method) (TomogramData class method) load_model() (in module cryovit.utils) load_sam_state_dict() (SAM2 method) load_state_dict() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) log_every_n_steps (BaseTrainer attribute) log_stats() (BaseModel method) logger (BaseExperimentConfig attribute) losses (BaseModel attribute) (BatchedModelResult attribute) lr (BaseModel attribute)

M

max_epochs (BaseTrainer attribute) memmap() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) memmap_() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) memmap_like() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) memmap_refresh_() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) metrics (BaseModel attribute) (BatchedModelResult attribute)

model (BaseExperimentConfig attribute) model_cfg (SavedModel attribute) model_dir (BaseModel attribute) (ExperimentPaths attribute) model_type (SavedModel attribute) ModelType (class in cryovit.types) module cryovit.config cryovit.datamodules cryovit.datasets cryovit.models cryovit.run cryovit.types cryovit.utils MultiSampleDataModule (class in cryovit.datamodules)

N

name (BaseExperimentConfig attribute) (BaseModel attribute) (SavedModel attribute)

num_slices (BatchedTomogramData property) num_tomos (BatchedModelResult attribute) (BatchedTomogramData property) nunique (FileMetadata attribute)

O

on_before_optimizer_step() (BaseModel method)

P

paths (BaseExperimentConfig attribute) (DinoFeaturesConfig attribute) precision (BaseTrainer attribute) predict_dataloader() (BaseDataModule method) (FileDataModule method)

predict_df() (BaseDataModule method) (FractionalSampleDataModule method) (MultiSampleDataModule method) (SingleSampleDataModule method) predict_step() (BaseModel method) preds (BatchedModelResult attribute)

R

random_seed (BaseExperimentConfig attribute) read_hdf() (in module cryovit.utils) read_mrc() (in module cryovit.utils) read_tiff() (in module cryovit.utils) results_dir (ExperimentPaths attribute)

resume_ckpt (BaseExperimentConfig attribute) run_dino() (in module cryovit.run) run_evaluation() (in module cryovit.run) run_inference() (in module cryovit.run) run_training() (in module cryovit.run)

S

SAM2 (class in cryovit.models) sample (BaseDataModule attribute) Sample (class in cryovit.types) sample (DinoFeaturesConfig attribute) (FileData attribute) samples (BatchedModelResult attribute) save() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) save_model() (in module cryovit.utils) save_model_from_weights() (in module cryovit.utils)

SavedModel (class in cryovit.utils) set() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) SingleSampleDataModule (class in cryovit.datamodules) split_id (BaseDataModule attribute) (BatchedModelResult attribute) split_key (BaseDataModule attribute) split_name (ExperimentPaths attribute) state_dict() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method)

T

test_dataloader() (BaseDataModule method) (FileDataModule method) test_df() (BaseDataModule method) (FractionalSampleDataModule method) (MultiSampleDataModule method) (SingleSampleDataModule method) test_sample (BaseDataModule attribute) test_step() (BaseModel method) to_tensordict() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method) tomo_name (ExperimentPaths attribute)

tomo_names (BatchedModelResult attribute) tomo_path (FileData attribute) TomoDataset (class in cryovit.datasets) TomogramData (class in cryovit.types) train_dataloader() (BaseDataModule method) (FileDataModule method) train_df() (BaseDataModule method) (FractionalSampleDataModule method) (MultiSampleDataModule method) (SingleSampleDataModule method) trainer (BaseExperimentConfig attribute) training_step() (BaseModel method)

U

unbind() (BatchedTomogramData method) (BatchedTomogramMetadata method) (TomogramData method)

UNet3D (class in cryovit.models)

V

val_dataloader() (BaseDataModule method) (FileDataModule method) val_df() (BaseDataModule method) (FractionalSampleDataModule method) (MultiSampleDataModule method) (SingleSampleDataModule method)

validate_dino_config() (in module cryovit.config) validate_experiment_config() (in module cryovit.config) validation_step() (BaseModel method) VITDataset (class in cryovit.datasets)

W

weight_decay (BaseModel attribute)

weights (SavedModel attribute)