Index

A

augment_dataset() (in module src.actions.dataset)

augment_image() (in module src.actions.dataset) augmentation_algorithm() (in module src.actions.dataset)

B

binarise_image() (in module src.helpers.describe_leaf) binarise_sequence() (src.data_model.data_model.MaskSequence method) bottleneck() (src.pipelines.tensorflow_v2.models.unet.UnetBlock method)

build() (src.pipelines.tensorflow_v2.models.hyper_unet.HyperUnet method) (src.pipelines.tensorflow_v2.models.hyper_unet_resnet.HyperUnetResnet method) (src.pipelines.tensorflow_v2.models.hyper_wnet.HyperWnet method)

C

call() (src.pipelines.tensorflow_v2.losses.custom_losses.FocalLoss method) (src.pipelines.tensorflow_v2.losses.custom_losses.FocalLossV2 method) (src.pipelines.tensorflow_v2.losses.custom_losses.SoftDiceLoss method) (src.pipelines.tensorflow_v2.losses.custom_losses.WeightedCE method) (src.pipelines.tensorflow_v2.models.hyper_unet_resnet.ResBlock method) (src.pipelines.tensorflow_v2.models.hyper_wnet.ConvBridgeBlock method) (src.pipelines.tensorflow_v2.models.unet.Unet method) (src.pipelines.tensorflow_v2.models.unet.UnetBlock method) (src.pipelines.tensorflow_v2.models.unet_resnet.ResBlock method) (src.pipelines.tensorflow_v2.models.unet_resnet.UnetResnet method) (src.pipelines.tensorflow_v2.models.wnet.ConvBridgeBlock method) (src.pipelines.tensorflow_v2.models.wnet.MiniUnet method) (src.pipelines.tensorflow_v2.models.wnet.WNet method)

check_model_save() (in module src.pipelines.tensorflow_v2.helpers.utilities) chip_image() (in module src.helpers.extract_dataset) chip_range() (in module src.helpers.extract_dataset) classification_report() (in module src.helpers.utilities) configure_for_performance() (in module src.pipelines.tensorflow_v2.helpers.utilities) ConvBridgeBlock (class in src.pipelines.tensorflow_v2.models.hyper_wnet) (class in src.pipelines.tensorflow_v2.models.wnet) create_dataset_structure() (in module src.actions.dataset) create_file_name() (in module src.helpers.utilities) create_mask() (src.data_model.data_model.Mask method) create_sequence_objects() (in module src.helpers.utilities) create_subfolders() (in module src.helpers.utilities) crop_img() (in module src.actions.dataset)

D

downblock() (src.pipelines.tensorflow_v2.models.unet.UnetBlock method)

downsample_dataset() (in module src.actions.dataset)

E

extract_changed_leaves() (src.data_model.data_model.LeafSequence method) extract_dataset() (in module src.actions.dataset) extract_full_databunch_df() (in module src.actions.eda) extract_full_eda_df() (in module src.actions.eda) extract_leaf_images() (in module src.actions.extraction)

extract_mask_from_multipage() (src.data_model.data_model.MaskSequence method) extract_me() (src.data_model.data_model.Leaf method) extract_multipage_mask_images() (in module src.actions.extraction) extract_tiles() (in module src.actions.extraction) extract_tiles_databunch_df() (in module src.actions.eda) extract_tiles_eda_df() (in module src.actions.eda)

F

flip_flop() (in module src.actions.dataset)

FocalLoss (class in src.pipelines.tensorflow_v2.losses.custom_losses) FocalLossV2 (class in src.pipelines.tensorflow_v2.losses.custom_losses)

G

gaussian_blur() (in module src.pipelines.tensorflow_v2.helpers.utilities) get_all_layers() (src.pipelines.tensorflow_v2.models.unet.Unet method) (src.pipelines.tensorflow_v2.models.unet_resnet.UnetResnet method) (src.pipelines.tensorflow_v2.models.wnet.MiniUnet method) (src.pipelines.tensorflow_v2.models.wnet.WNet method) get_class_weight() (in module src.pipelines.tensorflow_v2.helpers.utilities) get_databunch_dataframe() (src.data_model.data_model.Leaf method) (src.data_model.data_model.LeafSequence method) (src.data_model.data_model.Mask method) (src.data_model.data_model.MaskSequence method) get_embolism_percent() (in module src.helpers.describe_leaf) get_filepath_list() (in module src.pipelines.tensorflow_v2.helpers.train_test) get_increment() (src.pipelines.tensorflow_v2.callbacks.lr_range_test.LRRangeTest static method) get_intersection() (in module src.helpers.describe_leaf)

get_iou_score() (in module src.helpers.utilities) get_iterations() (src.pipelines.tensorflow_v2.callbacks.lr_range_test.LRRangeTest static method) (src.pipelines.tensorflow_v2.callbacks.one_cycle.OneCycleLR static method) get_lr() (src.pipelines.tensorflow_v2.callbacks.one_cycle.OneCycleLR method) get_model_pred_batch_loss() (in module src.pipelines.tensorflow_v2.helpers.utilities) get_momentum() (src.pipelines.tensorflow_v2.callbacks.one_cycle.OneCycleLR method) get_sorted_list() (in module src.pipelines.tensorflow_v2.helpers.utilities) get_tf_dataset() (in module src.pipelines.tensorflow_v2.helpers.train_test) get_tile_databunch_df() (src.data_model.data_model.LeafSequence method) (src.data_model.data_model.MaskSequence method) get_unique_leaf_range() (in module src.helpers.describe_leaf) get_unique_range() (in module src.helpers.describe_leaf) get_workaround_details() (in module src.actions.prediction) global_contrast_normalization() (in module src.pipelines.tensorflow_v2.helpers.utilities)

H

HyperUnet (class in src.pipelines.tensorflow_v2.models.hyper_unet)

HyperUnetResnet (class in src.pipelines.tensorflow_v2.models.hyper_unet_resnet) HyperWnet (class in src.pipelines.tensorflow_v2.models.hyper_wnet)

I

im2_lt_im1() (in module src.pipelines.tensorflow_v2.helpers.utilities)

interactive_prompt() (in module src.helpers.utilities) (in module src.pipelines.tensorflow_v2.helpers.utilities)

L

Leaf (class in src.data_model.data_model) LeafSequence (class in src.data_model.data_model) LeafTile (class in src.data_model.data_model) load_extracted_images() (src.data_model.data_model.Leaf method) (src.data_model.data_model.LeafSequence method) (src.data_model.data_model.Mask method) (src.data_model.data_model.MaskSequence method)

load_image_array() (src.data_model.data_model.LeafSequence method) (src.data_model.data_model.MaskSequence method) load_image_objects() (in module src.helpers.utilities) load_tile_sequence() (src.data_model.data_model.LeafSequence method) (src.data_model.data_model.MaskSequence method) LRRangeTest (class in src.pipelines.tensorflow_v2.callbacks.lr_range_test)

M

Mask (class in src.data_model.data_model) MaskSequence (class in src.data_model.data_model) MaskTile (class in src.data_model.data_model) MiniUnet (class in src.pipelines.tensorflow_v2.models.wnet) Model (class in src.model.model) model() (src.pipelines.tensorflow_v2.models.unet.Unet method) (src.pipelines.tensorflow_v2.models.unet_resnet.UnetResnet method) (src.pipelines.tensorflow_v2.models.wnet.MiniUnet method) (src.pipelines.tensorflow_v2.models.wnet.WNet method) module src.actions.dataset src.actions.eda src.actions.extraction src.actions.plots src.actions.prediction src.data_model.data_model src.helpers.describe_leaf src.helpers.extract_dataset src.helpers.utilities src.model.model src.pipelines.tensorflow_v2.callbacks.lr_range_test src.pipelines.tensorflow_v2.callbacks.one_cycle src.pipelines.tensorflow_v2.helpers.train_test src.pipelines.tensorflow_v2.helpers.utilities src.pipelines.tensorflow_v2.losses.custom_losses src.pipelines.tensorflow_v2.models.hyper_unet src.pipelines.tensorflow_v2.models.hyper_unet_resnet src.pipelines.tensorflow_v2.models.hyper_wnet src.pipelines.tensorflow_v2.models.unet src.pipelines.tensorflow_v2.models.unet_resnet src.pipelines.tensorflow_v2.models.wnet

move_data() (in module src.actions.dataset)

O

on_train_batch_end() (src.pipelines.tensorflow_v2.callbacks.lr_range_test.LRRangeTest method) (src.pipelines.tensorflow_v2.callbacks.one_cycle.OneCycleLR method)

on_train_begin() (src.pipelines.tensorflow_v2.callbacks.one_cycle.OneCycleLR method) OneCycleLR (class in src.pipelines.tensorflow_v2.callbacks.one_cycle)

P

pad_chip() (in module src.helpers.extract_dataset) parse_arguments() (in module src.helpers.utilities) (in module src.pipelines.tensorflow_v2.helpers.utilities) parse_image_fc() (in module src.pipelines.tensorflow_v2.helpers.utilities) parse_numpy_image() (in module src.pipelines.tensorflow_v2.helpers.utilities) plot_embolism_profile() (in module src.actions.plots) plot_embolisms_per_leaf() (in module src.actions.plots) plot_LRTest() (src.pipelines.tensorflow_v2.callbacks.lr_range_test.LRRangeTest method) plot_mseq_embolism_counts() (in module src.actions.plots) plot_mseq_profiles() (in module src.actions.plots) plot_ocp_lr() (src.pipelines.tensorflow_v2.callbacks.one_cycle.OneCycleLR method) plot_ocp_lr_momentum() (src.pipelines.tensorflow_v2.callbacks.one_cycle.OneCycleLR method)

plot_ocp_momentum() (src.pipelines.tensorflow_v2.callbacks.one_cycle.OneCycleLR method) predict_leaf() (src.data_model.data_model.Leaf method) predict_leaf_sequence() (src.data_model.data_model.LeafSequence method) predict_tensorflow() (in module src.actions.prediction) predict_tile() (src.data_model.data_model.LeafTile method) (src.model.model.Model method) print_all_layers() (src.pipelines.tensorflow_v2.models.unet.Unet method) (src.pipelines.tensorflow_v2.models.unet_resnet.UnetResnet method) (src.pipelines.tensorflow_v2.models.wnet.MiniUnet method) (src.pipelines.tensorflow_v2.models.wnet.WNet method) print_options_dict() (in module src.helpers.utilities) (in module src.pipelines.tensorflow_v2.helpers.utilities)

R

read_file() (in module src.pipelines.tensorflow_v2.helpers.utilities) requirements() (in module src.helpers.utilities)

ResBlock (class in src.pipelines.tensorflow_v2.models.hyper_unet_resnet) (class in src.pipelines.tensorflow_v2.models.unet_resnet) rotate_img() (in module src.actions.dataset)

S

save_compilation_dict() (in module src.pipelines.tensorflow_v2.helpers.utilities) save_image() (in module src.actions.dataset) save_lrt_results() (in module src.pipelines.tensorflow_v2.helpers.utilities) save_prcurve_csv() (in module src.pipelines.tensorflow_v2.helpers.utilities) save_predictions() (in module src.pipelines.tensorflow_v2.helpers.utilities) shear_img() (in module src.actions.dataset) SoftDiceLoss (class in src.pipelines.tensorflow_v2.losses.custom_losses) split_dataset() (in module src.actions.dataset) src.actions.dataset module src.actions.eda module src.actions.extraction module src.actions.plots module src.actions.prediction module src.data_model.data_model module src.helpers.describe_leaf module src.helpers.extract_dataset module src.helpers.utilities module

src.model.model module src.pipelines.tensorflow_v2.callbacks.lr_range_test module src.pipelines.tensorflow_v2.callbacks.one_cycle module src.pipelines.tensorflow_v2.helpers.train_test module src.pipelines.tensorflow_v2.helpers.utilities module src.pipelines.tensorflow_v2.losses.custom_losses module src.pipelines.tensorflow_v2.models.hyper_unet module src.pipelines.tensorflow_v2.models.hyper_unet_resnet module src.pipelines.tensorflow_v2.models.hyper_wnet module src.pipelines.tensorflow_v2.models.unet module src.pipelines.tensorflow_v2.models.unet_resnet module src.pipelines.tensorflow_v2.models.wnet module

T

threshold() (in module src.pipelines.tensorflow_v2.helpers.utilities) tile_me() (src.data_model.data_model.Leaf method) (src.data_model.data_model.Mask method)

translate_img() (in module src.actions.dataset) trim_image_array() (in module src.helpers.utilities) trim_sequence_images() (in module src.helpers.utilities) tune_model() (in module src.pipelines.tensorflow_v2.helpers.utilities)

U

Unet (class in src.pipelines.tensorflow_v2.models.unet) UnetBlock (class in src.pipelines.tensorflow_v2.models.unet)

UnetResnet (class in src.pipelines.tensorflow_v2.models.unet_resnet) upblock() (src.pipelines.tensorflow_v2.models.unet.UnetBlock method) update_plot_format() (in module src.helpers.utilities)

W

WeightedCE (class in src.pipelines.tensorflow_v2.losses.custom_losses)

WNet (class in src.pipelines.tensorflow_v2.models.wnet)

Z

zoom_in_out() (in module src.actions.dataset)