Index

A

AbstractDatamodule (class in datamodules.base_datamodule) AbstractTask (class in tasks.base_task) Adaptive_Unet (class in models.backbones.adaptive_unet)

argmax_onehot() (in module datamodules.utils.functional) ASPP (class in models.backbones.deeplabv3_aspp) ASPP_Bottleneck (class in models.backbones.deeplabv3_aspp)

B

Baby_UNet (class in models.backbones.unet) BackboneHeaderModel (class in models.backbone_header_model)

BasicBlock (class in models.backbones.deeplabv3_resnet) Bottleneck (class in models.backbones.deeplabv3_resnet)

C

callbacks module callbacks.general_callbacks module callbacks.model_callbacks module callbacks.wandb_callbacks module check_config() (in module utils.utils) check_min_num_samples() (AbstractDatamodule static method) check_missing_analytics() (in module datamodules.utils.misc) CheckBackboneHeaderCompatibility (class in callbacks.model_callbacks) Classification (class in tasks.classification.classification)

ClassificationDatamodule (class in datamodules.Classification.datamodule) CNN_basic (class in models.backbones.baby_cnn) compute() (HisDBIoU method) compute_mean_std() (in module datamodules.utils.image_analytics) configure_optimizers() (AbstractTask method) conv1 (CNN_basic attribute) conv2 (CNN_basic attribute) conv3 (CNN_basic attribute) conv3x3() (in module models.backbones.resnet) (in module models.backbones.resnetdd) ConvPoolHeader (class in models.headers.unet) CroppedDatasetRGB (class in datamodules.RGB.datasets.cropped_dataset) CroppedHisDBDataset (class in datamodules.DivaHisDB.datasets.cropped_dataset) CroppedRotNet (class in datamodules.RotNet.datasets.cropped_dataset)

D

data_root (DatasetSpecs attribute) DataModuleCroppedRGB (class in datamodules.RGB.datamodule_cropped) DataModuleIndexed (class in datamodules.IndexedFormats.datamodule) DataModuleRGB (class in datamodules.RGB.datamodule) DataModuleRolfFormat (class in datamodules.RolfFormat.datamodule) datamodules module datamodules.base_datamodule module datamodules.Classification module datamodules.Classification.datamodule module datamodules.Classification.utils module datamodules.Classification.utils.image_analytics module datamodules.Classification.utils.misc module datamodules.DivaHisDB module datamodules.DivaHisDB.datamodule_cropped module datamodules.DivaHisDB.datasets module datamodules.DivaHisDB.datasets.cropped_dataset module datamodules.DivaHisDB.utils module datamodules.DivaHisDB.utils.functional module datamodules.DivaHisDB.utils.image_analytics module datamodules.DivaHisDB.utils.output_tools module datamodules.DivaHisDB.utils.single_transform module datamodules.IndexedFormats module datamodules.IndexedFormats.datamodule module datamodules.IndexedFormats.datasets module datamodules.IndexedFormats.datasets.full_page_dataset module datamodules.IndexedFormats.utils module datamodules.IndexedFormats.utils.image_analytics module datamodules.IndexedFormats.utils.output_tools module datamodules.RGB module datamodules.RGB.datamodule module datamodules.RGB.datamodule_cropped module datamodules.RGB.datasets module datamodules.RGB.datasets.cropped_dataset module datamodules.RGB.datasets.full_page_dataset module datamodules.RGB.utils module datamodules.RGB.utils.functional module datamodules.RGB.utils.image_analytics module datamodules.RGB.utils.output_tools module

datamodules.RGB.utils.single_transform module datamodules.RolfFormat module datamodules.RolfFormat.datamodule module datamodules.RolfFormat.datasets module datamodules.RolfFormat.datasets.dataset module datamodules.RolfFormat.utils module datamodules.RolfFormat.utils.image_analytics module datamodules.RotNet module datamodules.RotNet.datamodule_cropped module datamodules.RotNet.datasets module datamodules.RotNet.datasets.cropped_dataset module datamodules.RotNet.utils module datamodules.RotNet.utils.image_analytics module datamodules.RotNet.utils.misc module datamodules.utils module datamodules.utils.dataset_predict module datamodules.utils.exceptions module datamodules.utils.functional module datamodules.utils.image_analytics module datamodules.utils.misc module datamodules.utils.output_tools module datamodules.utils.single_transforms module datamodules.utils.twin_transforms module datamodules.utils.wrapper_transforms module DatasetIndexed (class in datamodules.IndexedFormats.datasets.full_page_dataset) DatasetPredict (class in datamodules.utils.dataset_predict) DatasetRGB (class in datamodules.RGB.datasets.full_page_dataset) DatasetRolfFormat (class in datamodules.RolfFormat.datasets.dataset) DatasetSpecs (class in datamodules.RolfFormat.datasets.dataset) decoding_block() (in module models.backbones.adaptive_unet) (in module models.backbones.doc_ufcn) DeepLabV3 (class in models.backbones.deeplabv3) deeplabv3() (in module models.backbones.deeplabv3) deeplabv3_builder() (in module models.backbones.deeplabv3) deeplabv3_resnet101_os16() (in module models.backbones.deeplabv3) deeplabv3_resnet152_os16() (in module models.backbones.deeplabv3) deeplabv3_resnet18_os16() (in module models.backbones.deeplabv3) deeplabv3_resnet18_os8() (in module models.backbones.deeplabv3) deeplabv3_resnet34_os16() (in module models.backbones.deeplabv3) deeplabv3_resnet34_os8() (in module models.backbones.deeplabv3) deeplabv3_resnet50_os16() (in module models.backbones.deeplabv3) dil_block() (in module models.backbones.doc_ufcn) DivaHisDBDataModuleCropped (class in datamodules.DivaHisDB.datamodule_cropped) doc_dir (DatasetSpecs attribute) doc_names (DatasetSpecs attribute) Doc_ufcn (class in models.backbones.doc_ufcn) DoubleConv (class in models.backbones.unet) Down (class in models.backbones.unet)

E

empty() (in module utils.utils) encoding_block() (in module models.backbones.adaptive_unet) (in module models.backbones.doc_ufcn) (in module models.backbones.unet) encoding_block1() (in module models.backbones.adaptive_unet) execute module

execute() (in module execute) expansion (BasicBlock attribute) (Bottleneck attribute) expected_input_size (CNN_basic attribute) expend_glob_path_list() (DatasetPredict static method)

F

fc (CNN_basic attribute) FCNHead (class in models.headers.fully_connected) find_new_filename() (in module datamodules.utils.misc) finish() (in module utils.utils) forward() (AbstractTask method) (Adaptive_Unet method) (ASPP method) (ASPP_Bottleneck method) (BackboneHeaderModel method) (BasicBlock method) (Bottleneck method) (Classification method) (CNN_basic method) (ConvPoolHeader method) (DeepLabV3 method) (Doc_ufcn method) (DoubleConv method) (Down method) (OldUNet method) (PoolHeader method) (ResNet method), [1] (ResNet_BasicBlock_OS16 method) (ResNet_BasicBlock_OS8 method) (ResNet_Bottleneck_OS16 method) (ResNetFCNHead method) (ResNetHeader method) (SegNet method) (SemanticSegmentationRGB method) (SingleLinear method) (UNet method) (Unet method) (UnetDownModule method) (UnetEncoder method) (UNetFCNHead method) (UNetNajoua method) (Up method) (UpsampleBlock method) (VGG method)

forward_backbone() (Unet method) freeze_encoder() (Unet method)

G

get_analytics() (in module datamodules.DivaHisDB.utils.image_analytics) (in module datamodules.IndexedFormats.utils.image_analytics) (in module datamodules.RGB.utils.image_analytics) get_analytics_data() (in module datamodules.RolfFormat.utils.image_analytics) (in module datamodules.RotNet.utils.image_analytics) get_analytics_data_image_folder() (in module datamodules.Classification.utils.image_analytics) get_analytics_gt() (in module datamodules.RolfFormat.utils.image_analytics) get_backbone() (in module models.backbones.backboned_unet) get_callable_dict() (in module tasks.utils.task_utils) get_callable_name() (in module tasks.utils.task_utils) get_cityscapes_model_path() (in module models.backbones.deeplabv3) get_class_weights() (in module datamodules.DivaHisDB.utils.image_analytics) (in module datamodules.RGB.utils.image_analytics) get_gt_data_paths() (CroppedDatasetRGB static method) (CroppedRotNet static method) get_image_dims() (in module datamodules.utils.misc) get_img_gt_path_list() (DatasetIndexed static method) (DatasetRGB static method) (DatasetRolfFormat static method)

get_img_name_coordinates() (DataModuleCroppedRGB method) (DivaHisDBDataModuleCropped method) get_logger() (in module utils.utils) get_output_file_list() (in module datamodules.utils.misc) get_output_filename_predict() (DataModuleIndexed method) (DataModuleRGB method) (DataModuleRolfFormat method) get_output_filename_test() (DataModuleIndexed method) (DataModuleRGB method) (DataModuleRolfFormat method) get_params() (TwinRandomCrop method) get_wandb_logger() (in module callbacks.wandb_callbacks) gt_dir (DatasetSpecs attribute) gt_names (DatasetSpecs attribute) gt_to_int_encoding() (in module datamodules.DivaHisDB.utils.functional) (in module datamodules.RGB.utils.functional) gt_to_one_hot() (in module datamodules.DivaHisDB.utils.functional) (in module datamodules.RGB.utils.functional)

H

height (ImageDimensions attribute)

HisDBIoU (class in metrics.divahisdb)

I

ImageDimensions (class in datamodules.utils.misc) infer_skip_channels() (Unet method)

initialize_weights() (in module models.backbones.segnet) IntegerEncoding (class in datamodules.DivaHisDB.utils.single_transform) (class in datamodules.RGB.utils.single_transform)

L

LOG (OutputKeys attribute)

log_hyperparameters() (in module utils.utils) LOSS (OutputKeys attribute)

M

make_layer() (in module models.backbones.deeplabv3_resnet) make_layers() (in module models.backbones.VGG) merge_patches() (in module datamodules.utils.output_tools) metrics module metrics.divahisdb module models module models.backbone_header_model module models.backbones module models.backbones.adaptive_unet module models.backbones.baby_cnn module models.backbones.backboned_unet module models.backbones.deeplabv3 module models.backbones.deeplabv3_aspp module models.backbones.deeplabv3_resnet module models.backbones.doc_ufcn module models.backbones.resnet module models.backbones.resnetdd module models.backbones.segnet module models.backbones.unet module models.backbones.VGG module models.headers module models.headers.fully_connected module models.headers.fully_convolution module models.headers.unet module module callbacks callbacks.general_callbacks callbacks.model_callbacks callbacks.wandb_callbacks datamodules datamodules.base_datamodule datamodules.Classification datamodules.Classification.datamodule datamodules.Classification.utils datamodules.Classification.utils.image_analytics datamodules.Classification.utils.misc datamodules.DivaHisDB datamodules.DivaHisDB.datamodule_cropped datamodules.DivaHisDB.datasets datamodules.DivaHisDB.datasets.cropped_dataset datamodules.DivaHisDB.utils datamodules.DivaHisDB.utils.functional datamodules.DivaHisDB.utils.image_analytics datamodules.DivaHisDB.utils.output_tools datamodules.DivaHisDB.utils.single_transform datamodules.IndexedFormats datamodules.IndexedFormats.datamodule datamodules.IndexedFormats.datasets datamodules.IndexedFormats.datasets.full_page_dataset datamodules.IndexedFormats.utils datamodules.IndexedFormats.utils.image_analytics datamodules.IndexedFormats.utils.output_tools datamodules.RGB datamodules.RGB.datamodule datamodules.RGB.datamodule_cropped datamodules.RGB.datasets datamodules.RGB.datasets.cropped_dataset datamodules.RGB.datasets.full_page_dataset datamodules.RGB.utils datamodules.RGB.utils.functional datamodules.RGB.utils.image_analytics datamodules.RGB.utils.output_tools datamodules.RGB.utils.single_transform datamodules.RolfFormat datamodules.RolfFormat.datamodule datamodules.RolfFormat.datasets datamodules.RolfFormat.datasets.dataset datamodules.RolfFormat.utils datamodules.RolfFormat.utils.image_analytics datamodules.RotNet datamodules.RotNet.datamodule_cropped datamodules.RotNet.datasets datamodules.RotNet.datasets.cropped_dataset datamodules.RotNet.utils datamodules.RotNet.utils.image_analytics datamodules.RotNet.utils.misc datamodules.utils datamodules.utils.dataset_predict datamodules.utils.exceptions datamodules.utils.functional datamodules.utils.image_analytics datamodules.utils.misc datamodules.utils.output_tools datamodules.utils.single_transforms datamodules.utils.twin_transforms datamodules.utils.wrapper_transforms execute metrics metrics.divahisdb models models.backbone_header_model models.backbones models.backbones.adaptive_unet models.backbones.baby_cnn models.backbones.backboned_unet models.backbones.deeplabv3 models.backbones.deeplabv3_aspp models.backbones.deeplabv3_resnet models.backbones.doc_ufcn models.backbones.resnet models.backbones.resnetdd models.backbones.segnet models.backbones.unet models.backbones.VGG models.headers models.headers.fully_connected models.headers.fully_convolution models.headers.unet tasks tasks.base_task tasks.classification tasks.classification.classification tasks.DivaHisDB tasks.DivaHisDB.semantic_segmentation_cropped tasks.RGB tasks.RGB.semantic_segmentation tasks.RGB.semantic_segmentation_cropped tasks.utils tasks.utils.outputs tasks.utils.task_utils utils utils.utils

MorphoBuilding (class in datamodules.utils.single_transforms)

O

OldUNet (class in models.backbones.unet) on_predict_start() (SemanticSegmentationRGB method) on_test_end() (SemanticSegmentationCroppedHisDB method) (SemanticSegmentationCroppedRGB method) (SemanticSegmentationRGB method) on_test_epoch_end() (TimeTracker method) on_test_epoch_start() (TimeTracker method) on_test_start() (SemanticSegmentationRGB method) on_train_epoch_end() (TimeTracker method) on_train_epoch_start() (TimeTracker method) on_train_start() (TimeTracker method) (WatchModelWithWandb method)

one_conv1() (in module models.backbones.unet) one_conv2() (in module models.backbones.unet) OneHotEncoding (class in datamodules.DivaHisDB.utils.single_transform) (class in datamodules.RGB.utils.single_transform) OneHotToPixelLabelling (class in datamodules.utils.single_transforms) OnlyImage (class in datamodules.utils.wrapper_transforms) OnlyTarget (class in datamodules.utils.wrapper_transforms) output_to_class_encodings() (in module datamodules.DivaHisDB.utils.output_tools) (in module datamodules.RGB.utils.output_tools) OutputKeys (class in tasks.utils.outputs)

P

PathMissingDirinSplitDir PathMissingSplitDir PathNone PathNotDir pil_loader_gif() (in module datamodules.utils.misc) PoolHeader (class in models.headers.unet) predict_dataloader() (DataModuleIndexed method) (DataModuleRGB method) (DataModuleRolfFormat method)

predict_step() (AbstractTask method) (SemanticSegmentationRGB method) PREDICTION (OutputKeys attribute) print_config() (in module utils.utils) print_merge_tool_info() (in module tasks.utils.task_utils)

R

range_from (DatasetSpecs attribute) range_to (DatasetSpecs attribute) reduce_dict() (in module tasks.utils.outputs) ResNet (class in models.backbones.resnet) (class in models.backbones.resnetdd) ResNet101 (class in models.backbones.resnet) resnet101() (in module models.backbones.resnetdd) ResNet101_OS16() (in module models.backbones.deeplabv3_resnet) ResNet152 (class in models.backbones.resnet) resnet152() (in module models.backbones.resnetdd) ResNet152_OS16() (in module models.backbones.deeplabv3_resnet) ResNet18 (class in models.backbones.resnet) resnet18() (in module models.backbones.resnetdd) ResNet18_OS16() (in module models.backbones.deeplabv3_resnet)

ResNet18_OS8() (in module models.backbones.deeplabv3_resnet) ResNet34 (class in models.backbones.resnet) resnet34() (in module models.backbones.resnetdd) ResNet34_OS16() (in module models.backbones.deeplabv3_resnet) ResNet34_OS8() (in module models.backbones.deeplabv3_resnet) ResNet50 (class in models.backbones.resnet) resnet50() (in module models.backbones.resnetdd) ResNet50_OS16() (in module models.backbones.deeplabv3_resnet) ResNet_BasicBlock_OS16 (class in models.backbones.deeplabv3_resnet) ResNet_BasicBlock_OS8 (class in models.backbones.deeplabv3_resnet) ResNet_Bottleneck_OS16 (class in models.backbones.deeplabv3_resnet) ResNetFCNHead (class in models.headers.fully_convolution) ResNetHeader (class in models.headers.fully_connected) RightAngleRotation (class in datamodules.utils.single_transforms) RotNetDivaHisDBDataModuleCropped (class in datamodules.RotNet.datamodule_cropped)

S

save_json() (in module datamodules.utils.misc) save_numpy_files() (in module tasks.utils.outputs) save_output_page_image() (in module datamodules.DivaHisDB.utils.output_tools) (in module datamodules.IndexedFormats.utils.output_tools) (in module datamodules.RGB.utils.output_tools) SaveModelStateDictAndTaskCheckpoint (class in callbacks.model_callbacks) SegNet (class in models.backbones.segnet) selection_validation() (in module datamodules.utils.misc) SemanticSegmentationCroppedHisDB (class in tasks.DivaHisDB.semantic_segmentation_cropped) SemanticSegmentationCroppedRGB (class in tasks.RGB.semantic_segmentation_cropped) SemanticSegmentationRGB (class in tasks.RGB.semantic_segmentation) setup() (AbstractDatamodule method) (AbstractTask method) (CheckBackboneHeaderCompatibility method) (Classification method) (ClassificationDatamodule method) (DataModuleCroppedRGB method) (DataModuleIndexed method) (DataModuleRGB method) (DataModuleRolfFormat method) (DivaHisDBDataModuleCropped method) (RotNetDivaHisDBDataModuleCropped method) (SemanticSegmentationCroppedHisDB method) (SemanticSegmentationCroppedRGB method) (SemanticSegmentationRGB method)

SingleLinear (class in models.headers.fully_connected) step() (AbstractTask method)

T

TARGET (OutputKeys attribute) tasks module tasks.base_task module tasks.classification module tasks.classification.classification module tasks.DivaHisDB module tasks.DivaHisDB.semantic_segmentation_cropped module tasks.RGB module tasks.RGB.semantic_segmentation module tasks.RGB.semantic_segmentation_cropped module tasks.utils module tasks.utils.outputs module tasks.utils.task_utils module test_dataloader() (ClassificationDatamodule method) (DataModuleCroppedRGB method) (DataModuleIndexed method) (DataModuleRGB method) (DataModuleRolfFormat method) (DivaHisDBDataModuleCropped method) (RotNetDivaHisDBDataModuleCropped method) test_epoch_end() (AbstractTask method) test_step() (AbstractTask method) (Classification method) (SemanticSegmentationCroppedHisDB method) (SemanticSegmentationCroppedRGB method) (SemanticSegmentationRGB method) TilesBuilding (class in datamodules.utils.single_transforms) TimeTracker (class in callbacks.general_callbacks) to_loss_format() (AbstractTask static method) to_metrics_format() (AbstractTask static method) (SemanticSegmentationCroppedHisDB static method) (SemanticSegmentationCroppedRGB static method) (SemanticSegmentationRGB static method) ToTensorSlidingWindowCrop (class in datamodules.utils.twin_transforms) train_dataloader() (ClassificationDatamodule method) (DataModuleCroppedRGB method) (DataModuleIndexed method) (DataModuleRGB method) (DataModuleRolfFormat method) (DivaHisDBDataModuleCropped method) (RotNetDivaHisDBDataModuleCropped method)

training (AbstractTask attribute) (Adaptive_Unet attribute) (ASPP attribute) (ASPP_Bottleneck attribute) (Baby_UNet attribute) (BackboneHeaderModel attribute) (BasicBlock attribute) (Bottleneck attribute) (Classification attribute) (CNN_basic attribute) (ConvPoolHeader attribute) (DeepLabV3 attribute) (Doc_ufcn attribute) (DoubleConv attribute) (Down attribute) (OldUNet attribute) (PoolHeader attribute) (ResNet attribute), [1] (ResNet101 attribute) (ResNet152 attribute) (ResNet18 attribute) (ResNet34 attribute) (ResNet50 attribute) (ResNet_BasicBlock_OS16 attribute) (ResNet_BasicBlock_OS8 attribute) (ResNet_Bottleneck_OS16 attribute) (ResNetHeader attribute) (SegNet attribute) (SemanticSegmentationCroppedHisDB attribute) (SemanticSegmentationCroppedRGB attribute) (SemanticSegmentationRGB attribute) (SingleLinear attribute) (UNet attribute) (Unet attribute) (UNet16 attribute) (UNet32 attribute) (UNet64 attribute) (UnetDownModule attribute) (UnetEncoder attribute) (UNetFCNHead attribute) (UNetNajoua attribute) (Up attribute) (UpsampleBlock attribute) (VGG attribute) training_step() (AbstractTask method) (Classification method) (SemanticSegmentationCroppedHisDB method) (SemanticSegmentationCroppedRGB method) (SemanticSegmentationRGB method) TwinCompose (class in datamodules.utils.twin_transforms) TwinImageToTensor (class in datamodules.utils.twin_transforms) TwinRandomCrop (class in datamodules.utils.twin_transforms)

U

Unet (class in models.backbones.backboned_unet) UNet (class in models.backbones.unet) UNet16 (class in models.backbones.unet) UNet32 (class in models.backbones.unet) UNet64 (class in models.backbones.unet) UnetDownModule (class in models.backbones.backboned_unet) UnetEncoder (class in models.backbones.backboned_unet) UNetFCNHead (class in models.headers.unet)

UNetNajoua (class in models.backbones.unet) Up (class in models.backbones.unet) update() (HisDBIoU method) UpsampleBlock (class in models.backbones.backboned_unet) utils module utils.utils module

V

val_dataloader() (ClassificationDatamodule method) (DataModuleCroppedRGB method) (DataModuleIndexed method) (DataModuleRGB method) (DataModuleRolfFormat method) (DivaHisDBDataModuleCropped method) (RotNetDivaHisDBDataModuleCropped method) validate_path_for_classification() (in module datamodules.Classification.utils.misc) validate_path_for_segmentation() (in module datamodules.utils.misc) validate_path_for_self_supervised() (in module datamodules.RotNet.utils.misc) validation_epoch_end() (AbstractTask method) validation_step() (AbstractTask method) (Classification method) (SemanticSegmentationCroppedHisDB method) (SemanticSegmentationCroppedRGB method) (SemanticSegmentationRGB method)

VGG (class in models.backbones.VGG) vgg11() (in module models.backbones.VGG) vgg11_bn() (in module models.backbones.VGG) vgg13() (in module models.backbones.VGG) vgg13_bn() (in module models.backbones.VGG) vgg16() (in module models.backbones.VGG) vgg16_bn() (in module models.backbones.VGG) vgg19() (in module models.backbones.VGG) vgg19_bn() (in module models.backbones.VGG)

W

WatchModelWithWandb (class in callbacks.wandb_callbacks)

width (ImageDimensions attribute) write_file_mapping() (SemanticSegmentationRGB static method)