Index

A

ArcMarginProduct (class in cellmaps_image_embedding.models) augment_default() (in module cellmaps_image_embedding.dataset) augment_fliplr() (in module cellmaps_image_embedding.dataset) augment_fliplr_transpose() (in module cellmaps_image_embedding.dataset)

augment_flipud() (in module cellmaps_image_embedding.dataset) augment_flipud_lr() (in module cellmaps_image_embedding.dataset) augment_flipud_lr_transpose() (in module cellmaps_image_embedding.dataset) augment_flipud_transpose() (in module cellmaps_image_embedding.dataset) augment_transpose() (in module cellmaps_image_embedding.dataset)

C

cellmaps_image_embedding module cellmaps_image_embedding.cellmaps_image_embeddingcmd module cellmaps_image_embedding.dataset module cellmaps_image_embedding.exceptions module cellmaps_image_embedding.models module

cellmaps_image_embedding.runner module CellmapsImageEmbedder (class in cellmaps_image_embedding.runner) CellMapsImageEmbeddingError class_densenet121_dropout() (in module cellmaps_image_embedding.models) class_densenet121_large_dropout() (in module cellmaps_image_embedding.models) class_resnet50_dropout() (in module cellmaps_image_embedding.models) crop_image() (cellmaps_image_embedding.dataset.ProteinDataset method)

D

DEFAULT_FOLD (cellmaps_image_embedding.runner.EmbeddingGenerator attribute) DensenetClass (class in cellmaps_image_embedding.models)

DensenetEmbeddingGenerator (class in cellmaps_image_embedding.runner) DIMENSIONS (cellmaps_image_embedding.runner.EmbeddingGenerator attribute)

E

EmbeddingGenerator (class in cellmaps_image_embedding.runner)

F

FakeEmbeddingGenerator (class in cellmaps_image_embedding.runner) forward() (cellmaps_image_embedding.models.ArcMarginProduct method) (cellmaps_image_embedding.models.DensenetClass method) (cellmaps_image_embedding.models.ResnetClass method)

G

generate_readme() (cellmaps_image_embedding.runner.CellmapsImageEmbedder method) get_datasets_that_need_to_be_registered() (cellmaps_image_embedding.runner.DensenetEmbeddingGenerator method) (cellmaps_image_embedding.runner.EmbeddingGenerator method) get_dimensions() (cellmaps_image_embedding.runner.EmbeddingGenerator method) get_fold() (cellmaps_image_embedding.runner.EmbeddingGenerator method)

get_image_embedding_file() (cellmaps_image_embedding.runner.CellmapsImageEmbedder method) get_image_probability_file() (cellmaps_image_embedding.runner.CellmapsImageEmbedder method) get_name_mapping() (cellmaps_image_embedding.runner.ImageEmbeddingFilterAndNameTranslator method) get_next_embedding() (cellmaps_image_embedding.runner.DensenetEmbeddingGenerator method) (cellmaps_image_embedding.runner.EmbeddingGenerator method) (cellmaps_image_embedding.runner.FakeEmbeddingGenerator method)

I

image_to_tensor() (cellmaps_image_embedding.dataset.ProteinDataset method)

ImageEmbeddingFilterAndNameTranslator (class in cellmaps_image_embedding.runner)

L

load_pretrained() (cellmaps_image_embedding.models.DensenetClass method) (cellmaps_image_embedding.models.ResnetClass method)

M

main() (in module cellmaps_image_embedding.cellmaps_image_embeddingcmd) module cellmaps_image_embedding cellmaps_image_embedding.cellmaps_image_embeddingcmd cellmaps_image_embedding.dataset cellmaps_image_embedding.exceptions cellmaps_image_embedding.models cellmaps_image_embedding.runner

P

ProteinDataset (class in cellmaps_image_embedding.dataset)

R

read_rgby() (cellmaps_image_embedding.dataset.ProteinDataset method) reset_parameters() (cellmaps_image_embedding.models.ArcMarginProduct method)

ResnetClass (class in cellmaps_image_embedding.models) run() (cellmaps_image_embedding.runner.CellmapsImageEmbedder method)

S

set_random_crop() (cellmaps_image_embedding.dataset.ProteinDataset method)

set_transform() (cellmaps_image_embedding.dataset.ProteinDataset method) SUFFIX (cellmaps_image_embedding.runner.EmbeddingGenerator attribute)