Index

_

__init__() (phenocoder.Phenocoder method)

__repr__() (phenocoder.Phenocoder method)

A

adata (phenocoder.Phenocoder attribute) (phenocoder.spatial.SpatialGraphAnalyzer attribute)

add_sdata() (phenocoder.Phenocoder method)

B

beta (phenocoder.model.CVAE attribute) build_decoder() (phenocoder.model.CondCVAE method) (phenocoder.model.CVAE method)

build_encoder() (phenocoder.model.CondCVAE method) (phenocoder.model.CVAE method)

C

chull_min_degree (phenocoder.spatial.SpatialGraphAnalyzer attribute) chull_min_nds (phenocoder.spatial.SpatialGraphAnalyzer attribute) cluster_key (phenocoder.spatial.SpatialGraphAnalyzer attribute)

CondCVAE (class in phenocoder.model) conv_layers (phenocoder.model.CVAE attribute) CVAE (class in phenocoder.model)

D

data_dir (phenocoder.Phenocoder attribute) data_generator_train (phenocoder.Phenocoder attribute) data_generator_val (phenocoder.Phenocoder attribute) DatasetLoader (class in phenocoder.generator)

decoder (phenocoder.model.CVAE attribute) dense_dim (phenocoder.model.CVAE attribute) df_conditions (phenocoder.Phenocoder attribute) dropout (phenocoder.model.CVAE attribute)

E

encode() (phenocoder.Phenocoder method)

encoder (phenocoder.model.CVAE attribute) extract_patch() (phenocoder.generator.PatchGenerator method)

F

filter() (phenocoder.sampling.SpatialSubunitSampler method)

G

generate_dataset() (phenocoder.generator.PatchGenerator method) (phenocoder.Phenocoder method) generate_image_stats() (phenocoder.generator.PatchGenerator method) get_centrality() (phenocoder.spatial.SpatialGraphAnalyzer method) get_chull() (phenocoder.spatial.SpatialGraphAnalyzer method) get_chulls_connected_components() (phenocoder.spatial.SpatialGraphAnalyzer method) get_connectivity() (phenocoder.spatial.SpatialGraphAnalyzer method)

get_counts() (phenocoder.spatial.SpatialGraphAnalyzer method) get_generators() (phenocoder.generator.DatasetLoader method) get_interactions() (phenocoder.spatial.SpatialGraphAnalyzer method) get_moran() (phenocoder.spatial.SpatialGraphAnalyzer method) get_moran_cluster() (phenocoder.spatial.SpatialGraphAnalyzer method) get_patches() (phenocoder.generator.PatchGenerator method) get_scaling_percentiles() (phenocoder.generator.PatchGenerator method) get_spatial_stats() (phenocoder.spatial.SpatialGraphAnalyzer method)

I

index (phenocoder.spatial.SpatialGraphAnalyzer attribute) init_patches() (phenocoder.generator.PatchGenerator method)

initialize_model() (phenocoder.Phenocoder method) input_shape (phenocoder.model.CVAE attribute)

L

latent_dim (phenocoder.model.CVAE attribute)

load_datasets() (phenocoder.generator.DatasetLoader method) load_model() (phenocoder.Phenocoder method)

M

metrics (phenocoder.model.CVAE property) model (phenocoder.Phenocoder attribute) model_config (phenocoder.Phenocoder attribute) model_dir (phenocoder.Phenocoder attribute) model_oh_enc (phenocoder.Phenocoder attribute)

module phenocoder.generator phenocoder.model phenocoder.sampling phenocoder.spatial phenocoder.utils

N

n_classes (phenocoder.model.CondCVAE attribute)

O

on_epoch_end() (phenocoder.generator.SequenceGenerator method)

P

partition() (phenocoder.sampling.SpatialSubunitSampler method) PatchGenerator (class in phenocoder.generator) Phenocoder (class in phenocoder) phenocoder.generator module phenocoder.model module phenocoder.sampling module

phenocoder.spatial module phenocoder.utils module plot_latent_space() (in module phenocoder.utils) plot_reconstructions() (in module phenocoder.utils) plot_to_image() (in module phenocoder.utils)

R

radii (phenocoder.spatial.SpatialGraphAnalyzer attribute)

results (phenocoder.spatial.SpatialGraphAnalyzer attribute) run() (phenocoder.spatial.SpatialGraphAnalyzer method)

S

sample() (phenocoder.sampling.SpatialSubunitSampler method) sample_key (phenocoder.Phenocoder attribute) Sampling (class in phenocoder.model) sdata (phenocoder.Phenocoder attribute) seed_generator (phenocoder.model.Sampling attribute) select_patches() (phenocoder.generator.PatchGenerator method) SequenceGenerator (class in phenocoder.generator) set_train_val_split() (phenocoder.generator.DatasetLoader method)

spatial_key (phenocoder.spatial.SpatialGraphAnalyzer attribute) spatial_message_passing() (in module phenocoder.spatial) spatialgraph_embedding() (phenocoder.Phenocoder method) spatialgraph_stats() (phenocoder.Phenocoder method) SpatialGraphAnalyzer (class in phenocoder.spatial) SpatialSubunitSampler (class in phenocoder.sampling) stats (phenocoder.spatial.SpatialGraphAnalyzer attribute) summarize_model() (phenocoder.Phenocoder method)

T

test_step() (phenocoder.model.CondCVAE method) (phenocoder.model.CVAE method) to_df() (phenocoder.sampling.SpatialSubunitSampler method) (phenocoder.spatial.SpatialGraphAnalyzer method)

train() (phenocoder.Phenocoder method) train_step() (phenocoder.model.CondCVAE method) (phenocoder.model.CVAE method)

V

VALID_STATS (phenocoder.spatial.SpatialGraphAnalyzer attribute)

W

write_patches() (phenocoder.generator.PatchGenerator method)

write_training_plots_to_tensorboard() (in module phenocoder.utils)