Index

A

accuracy_fn() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) analyze() (atomai.models.ParticleAnalyzer method) analyze_image() (atomai.stat.SlidingFFTNMF method) apply_background() (atomai.transforms.datatransform method) apply_blur() (atomai.transforms.datatransform method) apply_contrast() (atomai.transforms.datatransform method)

apply_gauss() (atomai.transforms.datatransform method) apply_imresize() (atomai.transforms.datatransform method) apply_jitter() (atomai.transforms.datatransform method) apply_poisson() (atomai.transforms.datatransform method) apply_rotation() (atomai.transforms.datatransform method) apply_sp() (atomai.transforms.datatransform method) apply_zoom() (atomai.transforms.datatransform method) ase_obj_adv() (in module atomai.utils) ase_obj_basic() (in module atomai.utils) atom2dgaussian() (atomai.utils.MakeAtom method)

B

BasePredictor (class in atomai.predictors) BaseTrainer (class in atomai.trainers)

batch_predict() (atomai.predictors.BasePredictor method) (atomai.predictors.ImSpecPredictor method) (atomai.predictors.SegPredictor method)

C

circularmask() (atomai.utils.MakeAtom method) compare_coordinates() (in module atomai.utils) compile_ensemble_trainer() (atomai.trainers.EnsembleTrainer method) compile_multi_model_trainer() (atomai.models.dklGPR method) compile_trainer() (atomai.models.dklGPR method) (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) (atomai.trainers.viBaseTrainer method)

compute_hist() (atomai.losses_metrics.IoU method) ConvBlock (class in atomai.nets) convDecoderNet (class in atomai.nets) convEncoderNet (class in atomai.nets) create_lattice_mask() (in module atomai.utils) create_multiclass_lattice_mask() (in module atomai.utils) crop_borders() (in module atomai.utils) cv_resize() (in module atomai.utils) cv_resize_stack() (in module atomai.utils) cv_thresh() (in module atomai.utils)

D

data_augmentation() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) dataloader() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) datatransform (class in atomai.transforms)

decode() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.nets.SignalED method) DenoisingAutoencoder (class in atomai.models) dice_loss (class in atomai.losses_metrics) DilatedBlock (class in atomai.nets) dilnet (class in atomai.nets) dklGPR (class in atomai.models)

E

elbo_fn() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method) embed() (atomai.models.dklGPR method) encode() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.nets.SignalED method) encode_() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) encode_image_() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) encode_images() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method)

encode_trajectories() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) ensemble_batch_predict() (atomai.predictors.EnsemblePredictor method) ensemble_forward() (atomai.predictors.EnsemblePredictor method) ensemble_forward_() (atomai.predictors.EnsemblePredictor method) ensemble_locate() (in module atomai.predictors) EnsemblePredictor (class in atomai.predictors) EnsembleTrainer (class in atomai.trainers) eval_model() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) evaluate() (atomai.losses_metrics.IoU method) evaluate_model() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method) extract_patches() (in module atomai.utils) extract_random_subimages() (in module atomai.utils) extract_subimages() (in module atomai.utils) extract_subimages_() (atomai.stat.imlocal method), [1]

F

fcDecoderNet (class in atomai.nets) fcEncoderNet (class in atomai.nets) FFTmask() (in module atomai.utils) FFTsub() (in module atomai.utils) filter_cells() (in module atomai.utils) find_com() (in module atomai.utils) fit() (atomai.models.DenoisingAutoencoder method) (atomai.models.dklGPR method) (atomai.models.ImSpec method) (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.Segmentor method) (atomai.models.VAE method) (atomai.stat.SpectralUnmixer method) (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method)

fit_ensemble() (atomai.models.dklGPR method) focal_loss (class in atomai.losses_metrics) forward_() (atomai.predictors.BasePredictor method) (atomai.predictors.ImSpecPredictor method) (atomai.predictors.SegPredictor method) forward_compute_elbo() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method)

G

gen_atom_mask() (atomai.utils.MakeAtom method) get_all_trajectories() (atomai.stat.imlocal method), [1] get_blob_params() (in module atomai.utils) get_loss_fn() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method)

get_nn_distances() (in module atomai.utils) get_nn_distances_() (in module atomai.utils) get_trajectory() (atomai.stat.imlocal class method), [1] gmm() (atomai.stat.imlocal method), [1]

I

ica() (atomai.stat.imlocal method), [1] imblock_ica() (atomai.stat.imlocal method), [1] imblock_nmf() (atomai.stat.imlocal method), [1] imblock_pca() (atomai.stat.imlocal method), [1] img_pad() (in module atomai.utils)

img_resize() (in module atomai.utils) imlocal (class in atomai.stat), [1] ImSpec (class in atomai.models) ImSpecPredictor (class in atomai.predictors) ImSpecTrainer (class in atomai.trainers) IoU (class in atomai.losses_metrics)

J

jrVAE (class in atomai.models)

jVAE (class in atomai.models)

K

kld_normal() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method)

L

load_ensemble() (in module atomai.models) load_model() (in module atomai.models) load_weights() (atomai.models.DenoisingAutoencoder method) (atomai.models.ImSpec method) (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.Segmentor method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method)

log_normal() (atomai.models.jrVAE class method) (atomai.models.jVAE class method) (atomai.models.rVAE class method) (atomai.models.VAE class method) (atomai.trainers.viBaseTrainer class method) log_unit_normal() (atomai.models.jrVAE class method) (atomai.models.jVAE class method) (atomai.models.rVAE class method) (atomai.models.VAE class method) (atomai.trainers.viBaseTrainer class method)

M

make_windows() (atomai.stat.SlidingFFTNMF method) MakeAtom (class in atomai.utils) manifold2d() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method)

manifold_traversal() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) map_bonds() (in module atomai.utils)

N

nmf() (atomai.stat.imlocal method), [1]

P

ParticleAnalyzer (class in atomai.models) particles_to_dataframe() (atomai.models.ParticleAnalyzer static method) pca() (atomai.stat.imlocal method), [1] pca_gmm() (atomai.stat.imlocal method), [1] pca_gmm_scree_plot() (atomai.stat.imlocal method), [1] pca_scree_plot() (atomai.stat.imlocal method), [1] peak_refinement() (in module atomai.utils) plot_decomposition_results() (atomai.stat.imlocal class method), [1] plot_results() (atomai.stat.SpectralUnmixer method) plot_trajectories() (in module atomai.utils) plot_trajectories_transitions() (in module atomai.utils) plot_transitions() (in module atomai.utils) predict() (atomai.models.DenoisingAutoencoder method) (atomai.models.dklGPR method) (atomai.models.ImSpec method) (atomai.models.Segmentor method) (atomai.predictors.BasePredictor method) (atomai.predictors.EnsemblePredictor method) (atomai.predictors.ImSpecPredictor method) (atomai.predictors.SegPredictor method)

preprocess() (atomai.predictors.BasePredictor method) (atomai.predictors.EnsemblePredictor method) (atomai.predictors.ImSpecPredictor method) (atomai.predictors.SegPredictor method) preprocess_train_data() (atomai.trainers.EnsembleTrainer method) print_statistics() (atomai.models.dklGPR method) (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) (atomai.trainers.viBaseTrainer method) process_fft() (atomai.stat.SlidingFFTNMF method)

R

rDecoderNet (class in atomai.nets) reconstruct() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) renumerate_classes() (atomai.stat.imlocal class method), [1] reparameterize() (atomai.models.jrVAE class method) (atomai.models.jVAE class method) (atomai.models.rVAE class method) (atomai.models.VAE class method) (atomai.trainers.viBaseTrainer class method) reparameterize_discrete() (atomai.models.jrVAE class method) (atomai.models.jVAE class method) (atomai.models.rVAE class method) (atomai.models.VAE class method) (atomai.trainers.viBaseTrainer class method)

ResBlock (class in atomai.nets) ResHedNet (class in atomai.nets) ResModule (class in atomai.nets) run() (atomai.models.dklGPR method) (atomai.predictors.ImSpecPredictor method) (atomai.predictors.SegPredictor method) (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) (atomai.transforms.datatransform method) run_nmf() (atomai.stat.SlidingFFTNMF method) rVAE (class in atomai.models)

S

sample_from_posterior() (atomai.models.dklGPR method) save_ensemble_metadict() (atomai.trainers.EnsembleTrainer method) save_model() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) (atomai.trainers.viBaseTrainer method) save_running_weights() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) save_weights() (atomai.models.dklGPR method) (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method) Segmentor (class in atomai.models) SegPredictor (class in atomai.predictors) SegResNet (class in atomai.nets) SegTrainer (class in atomai.trainers) select_lr() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) set_data() (atomai.models.dklGPR method) (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) (atomai.trainers.viBaseTrainer method)

set_decoder() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method) set_encoder() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method) set_model() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) (atomai.trainers.viBaseTrainer method) SignalDecoder (class in atomai.nets) SignalED (class in atomai.nets) SignalEncoder (class in atomai.nets) SlidingFFTNMF (class in atomai.stat) SpectralUnmixer (class in atomai.stat) stem_graphene() (in module atomai.utils.datasets) stem_smbfo() (in module atomai.utils.datasets) step() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) step_full() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method)

T

test_step() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) thompson() (atomai.models.dklGPR method) threshImg() (in module atomai.utils) threshold_() (atomai.losses_metrics.IoU class method) torch_format() (in module atomai.utils) train_baseline() (atomai.trainers.EnsembleTrainer method) train_ensemble_from_baseline() (atomai.trainers.EnsembleTrainer method) train_ensemble_from_scratch() (atomai.trainers.EnsembleTrainer method)

train_epoch() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method) (atomai.trainers.viBaseTrainer method) train_step() (atomai.models.dklGPR method) (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method) train_swag() (atomai.trainers.EnsembleTrainer method) transition_matrix() (atomai.stat.imlocal method), [1]

U

Unet (class in atomai.nets) update_classes() (in module atomai.stat) update_metadict() (atomai.models.jrVAE method) (atomai.models.jVAE method) (atomai.models.rVAE method) (atomai.models.VAE method)

update_training_parameters() (atomai.trainers.EnsembleTrainer method) UpsampleBlock (class in atomai.nets)

V

VAE (class in atomai.models) viBaseTrainer (class in atomai.trainers) visualize_manifold_learning() (atomai.models.jrVAE class method) (atomai.models.jVAE class method) (atomai.models.rVAE class method) (atomai.models.VAE class method)

visualize_particles() (atomai.models.ParticleAnalyzer static method)

W

weight_perturbation() (atomai.trainers.BaseTrainer method) (atomai.trainers.EnsembleTrainer method) (atomai.trainers.ImSpecTrainer method) (atomai.trainers.SegTrainer method)