Index

A

add_args() (Unet2D static method)

C

calculate_all_metrics() (in module rhizonet.metrics) common_files() (in module rhizonet.utils)

configure_optimizers() (Unet2D method) contrast_img() (in module rhizonet.utils) createBinaryAnnotation() (in module rhizonet.utils)

D

dynamic_scale() (in module rhizonet.unet2D)

E

elliptical_crop() (in module rhizonet.utils) evaluate() (in module rhizonet.metrics)

experiment (mySimpleLogger property) extract_largest_component_bbox_image() (in module rhizonet.utils)

F

finalize() (mySimpleLogger method)

forward() (Unet2D method)

G

get_biomass() (in module rhizonet.utils) get_data_transforms() (ImageDataset method) get_image_paths() (in module rhizonet.utils)

get_prediction() (in module rhizonet.predict) get_weights() (in module rhizonet.utils) getLargestCC() (in module rhizonet.postprocessing)

I

ImageDataset (class in rhizonet.unet2D)

L

log_dir (mySimpleLogger property) log_hyperparams() (mySimpleLogger method)

log_metrics() (mySimpleLogger method) loss_function() (Unet2D method)

M

main() (in module rhizonet.metrics) (in module rhizonet.postprocessing) (in module rhizonet.predict) (in module rhizonet.prepare_patches) (in module rhizonet.train) MapImage() (in module rhizonet.utils) maxProjection() (in module rhizonet.postprocessing) module rhizonet.metrics rhizonet.postprocessing rhizonet.predict rhizonet.prepare_patches rhizonet.simpleLogger rhizonet.train rhizonet.unet2D rhizonet.utils

mySimpleLogger (class in rhizonet.simpleLogger)

N

name (mySimpleLogger property)

O

on_test_epoch_end() (Unet2D method)

on_validation_epoch_end() (Unet2D method)

P

parse_prepare_variables() (in module rhizonet.prepare_patches) pred_function() (in module rhizonet.predict) (Unet2D method) PredDataset2D (class in rhizonet.unet2D)

predict_model() (in module rhizonet.predict) predict_step() (in module rhizonet.predict) (Unet2D method) prepare_patches() (in module rhizonet.prepare_patches) processing() (in module rhizonet.postprocessing)

R

rhizonet.metrics module rhizonet.postprocessing module rhizonet.predict module rhizonet.prepare_patches module

rhizonet.simpleLogger module rhizonet.train module rhizonet.unet2D module rhizonet.utils module

S

save() (mySimpleLogger method)

T

test_step() (Unet2D method) tiff_reader (class in rhizonet.unet2D) train_dataloader() (Unet2D method)

train_model() (in module rhizonet.train) training_step() (Unet2D method) transform_image() (in module rhizonet.predict)

U

Unet2D (class in rhizonet.unet2D)

V

val_dataloader() (Unet2D method)

validation_step() (Unet2D method) version (mySimpleLogger property)