Index

_

__del__() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) __init__() (biom3d.callbacks.Callback method) (biom3d.callbacks.Callbacks method) (biom3d.callbacks.DatasetSizeScheduler method) (biom3d.callbacks.ForceFGScheduler method) (biom3d.callbacks.GlobalScaleScheduler method) (biom3d.callbacks.ImageSaver method) (biom3d.callbacks.LogPrinter method) (biom3d.callbacks.LogSaver method) (biom3d.callbacks.LRSchedulerCosine method) (biom3d.callbacks.LRSchedulerMultiStep method) (biom3d.callbacks.LRSchedulerPoly method) (biom3d.callbacks.MetricsUpdater method) (biom3d.callbacks.ModelSaver method) (biom3d.callbacks.MomentumScheduler method) (biom3d.callbacks.OverlapScheduler method) (biom3d.callbacks.TensorboardSaver method) (biom3d.callbacks.WeightDecayScheduler method) (biom3d.datasets.semseg_batchgen.BatchGenDataLoader method) (biom3d.datasets.semseg_batchgen.Convert2DTo3DTransform method) (biom3d.datasets.semseg_batchgen.Convert3DTo2DTransform method) (biom3d.datasets.semseg_batchgen.DataReader method) (biom3d.datasets.semseg_batchgen.DictToTuple method) (biom3d.datasets.semseg_batchgen.DownsampleSegForDSTransform2 method) (biom3d.datasets.semseg_batchgen.MTBatchGenDataLoader method) (biom3d.datasets.semseg_batchgen.nnUNetRandomCropAndPadTransform method) (biom3d.datasets.semseg_batchgen.RandomCropAndPadTransform method) (biom3d.datasets.semseg_patch_fast.LabelToLong method) (biom3d.datasets.semseg_patch_fast.SemSeg3DPatchFast method) (biom3d.datasets.semseg_torchio.LabelToBool method) (biom3d.datasets.semseg_torchio.LabelToFloat method) (biom3d.datasets.semseg_torchio.LabelToLong method) (biom3d.datasets.semseg_torchio.RandomCropOrPad method) (biom3d.datasets.semseg_torchio.TorchioDataset method) (biom3d.datasets.semseg_torchio.TorchIOReaderWrapper method) (biom3d.metrics.CrossEntropy method) (biom3d.metrics.DC_and_CE_loss method) (biom3d.metrics.DeepMetric method) (biom3d.metrics.Dice method) (biom3d.metrics.DiceBCE method) (biom3d.metrics.IoU method) (biom3d.metrics.Metric method) (biom3d.metrics.MSE method) (biom3d.metrics.SoftDiceLoss method) (biom3d.models.decoder_vgg_deep.DecoderBlock method) (biom3d.models.decoder_vgg_deep.VGGDecoder method) (biom3d.models.encoder_efficientnet3d.EfficientNet3D method) (biom3d.models.encoder_efficientnet3d.MBConvBlock3D method) (biom3d.models.encoder_vgg.EncoderBlock method) (biom3d.models.encoder_vgg.GlobalAvgPool3d method) (biom3d.models.encoder_vgg.LambdaLayer method) (biom3d.models.encoder_vgg.SmallEncoderBlock method) (biom3d.models.encoder_vgg.VGGEncoder method) (biom3d.models.unet3d_eff.EffUNet method) (biom3d.models.unet3d_vgg_deep.UNet method) (biom3d.predictors.LoadImgPatch method) (biom3d.preprocess.Preprocessing method) (biom3d.utils.config.AttrDict method) (biom3d.utils.data_augmentation.SmartPatch method) (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) (biom3d.utils.time.Time method)

__iter__() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) __len__() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) __next__() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) _fg_path_root (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) _image_index (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) _images_path_root (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) _input_parse() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) _iterator (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) _masks_path_root (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) _output_parse() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) _output_parse_preprocess() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) _save() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) _saver (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) _size (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute)

A

abs_listdir() (in module biom3d.utils.os) abs_path() (in module biom3d.utils.os) adaptive_imread() (biom3d.utils.data_handler.file_handler.ImageManager static method) adaptive_imsave() (biom3d.utils.data_handler.file_handler.ImageManager static method)

adaptive_load_config() (in module biom3d.utils.config) apply_transform() (biom3d.datasets.semseg_torchio.RandomCropOrPad method) AttrDict (class in biom3d.utils.config) auto_config() (in module biom3d.auto_config) auto_config_preprocess() (in module biom3d.preprocess)

B

backward() (biom3d.models.encoder_efficientnet3d.SwishImplementation static method) BatchGenDataLoader (class in biom3d.datasets.semseg_batchgen) biom3d.auto_config module biom3d.callbacks module biom3d.datasets.semseg_batchgen module biom3d.datasets.semseg_patch_fast module biom3d.datasets.semseg_torchio module biom3d.eval module biom3d.metrics module biom3d.models.decoder_vgg_deep module biom3d.models.encoder_efficientnet3d module biom3d.models.encoder_vgg module biom3d.models.unet3d_eff module biom3d.models.unet3d_vgg_deep module biom3d.omero_downloader module biom3d.omero_pred module biom3d.pred module

biom3d.predictors module biom3d.preprocess module biom3d.preprocess_train module biom3d.train module biom3d.trainers module biom3d.utils.config module biom3d.utils.data_augmentation module biom3d.utils.decorators module biom3d.utils.encoding module biom3d.utils.filtering module biom3d.utils.fold module biom3d.utils.image module biom3d.utils.neural_network module biom3d.utils.os module biom3d.utils.time module BlockArgs() (in module biom3d.models.encoder_efficientnet3d) BlockDecoder (class in biom3d.models.encoder_efficientnet3d)

C

Callback (class in biom3d.callbacks) Callbacks (class in biom3d.callbacks) center() (in module biom3d.utils.filtering) centered_crop() (in module biom3d.datasets.semseg_batchgen) (in module biom3d.datasets.semseg_patch_fast) centered_pad() (in module biom3d.datasets.semseg_batchgen) (in module biom3d.datasets.semseg_patch_fast) (in module biom3d.utils.data_augmentation) close() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) closest() (in module biom3d.utils.filtering) compat_old_config() (in module biom3d.utils.config)

compute_median() (in module biom3d.auto_config) compute_otsu_criteria() (in module biom3d.utils.filtering) config_to_type() (in module biom3d.utils.config) configure_rotation_dummy_da_mirroring_and_inital_patch_size() (in module biom3d.datasets.semseg_batchgen) Convert2DTo3DTransform (class in biom3d.datasets.semseg_batchgen) Convert3DTo2DTransform (class in biom3d.datasets.semseg_batchgen) convert_num_pools() (in module biom3d.utils.neural_network) correct_mask() (in module biom3d.preprocess) create_save_dirs() (in module biom3d.utils.os) crop() (biom3d.datasets.semseg_torchio.RandomCropOrPad method) CrossEntropy (class in biom3d.metrics)

D

data_fingerprint() (in module biom3d.auto_config) DataHandlerFactory (class in biom3d.utils) DataReader (class in biom3d.datasets.semseg_batchgen) DatasetSizeScheduler (class in biom3d.callbacks) DC_and_CE_loss (class in biom3d.metrics) decode() (biom3d.models.encoder_efficientnet3d.BlockDecoder static method) DecoderBlock (class in biom3d.models.decoder_vgg_deep) DeepMetric (class in biom3d.metrics) deprecated() (in module biom3d.utils.decorators) Dice (class in biom3d.metrics) DiceBCE (class in biom3d.metrics)

DictToTuple (class in biom3d.datasets.semseg_batchgen) display_info() (in module biom3d.auto_config) display_mesh() (in module biom3d.utils.image) display_voxels() (in module biom3d.utils.image) dist_vec() (in module biom3d.utils.filtering) download_attachment() (in module biom3d.omero_downloader) download_datasets() (in module biom3d.omero_downloader) download_datasets_cli() (in module biom3d.omero_downloader) download_object() (in module biom3d.omero_downloader) download_object_cli() (in module biom3d.omero_downloader) DownsampleSegForDSTransform2 (class in biom3d.datasets.semseg_batchgen) drop_connect() (in module biom3d.models.encoder_efficientnet3d)

E

EfficientNet3D (class in biom3d.models.encoder_efficientnet3d) (class in biom3d.models.unet3d_eff) efficientnet3d() (in module biom3d.models.encoder_efficientnet3d) efficientnet_params() (in module biom3d.models.encoder_efficientnet3d) EffUNet (class in biom3d.models.unet3d_eff)

encode() (biom3d.models.encoder_efficientnet3d.BlockDecoder static method) EncoderBlock (class in biom3d.models.encoder_vgg) eval() (in module biom3d.eval) extract_features() (biom3d.models.encoder_efficientnet3d.EfficientNet3D method) extract_patch() (biom3d.datasets.semseg_torchio.RandomCropOrPad method)

F

fg (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) FG (biom3d.utils.data_handler.data_handler_abstract.OutputType attribute) find_patch_pool_batch() (in module biom3d.auto_config) ForceFGScheduler (class in biom3d.callbacks) foreground_crop() (in module biom3d.datasets.semseg_batchgen) (in module biom3d.datasets.semseg_patch_fast) forward() (biom3d.metrics.CrossEntropy method) (biom3d.metrics.DC_and_CE_loss method) (biom3d.metrics.DeepMetric method) (biom3d.metrics.Dice method) (biom3d.metrics.DiceBCE method) (biom3d.metrics.IoU method) (biom3d.metrics.Metric method) (biom3d.metrics.MSE method) (biom3d.metrics.RobustCrossEntropyLoss method) (biom3d.metrics.SoftDiceLoss method) (biom3d.models.decoder_vgg_deep.DecoderBlock method) (biom3d.models.decoder_vgg_deep.VGGDecoder method) (biom3d.models.encoder_efficientnet3d.EfficientNet3D method) (biom3d.models.encoder_efficientnet3d.MBConvBlock3D method) (biom3d.models.encoder_efficientnet3d.MemoryEfficientSwish method) (biom3d.models.encoder_efficientnet3d.Swish method) (biom3d.models.encoder_efficientnet3d.SwishImplementation static method) (biom3d.models.encoder_vgg.EncoderBlock method) (biom3d.models.encoder_vgg.GlobalAvgPool3d method) (biom3d.models.encoder_vgg.LambdaLayer method) (biom3d.models.encoder_vgg.SmallEncoderBlock method) (biom3d.models.encoder_vgg.VGGEncoder method) (biom3d.models.unet3d_eff.EffUNet method) (biom3d.models.unet3d_vgg_deep.UNet method)

freeze_encoder() (biom3d.models.unet3d_eff.EffUNet method) (biom3d.models.unet3d_vgg_deep.UNet method) from_name() (biom3d.models.encoder_efficientnet3d.EfficientNet3D class method)

G

generate_kfold_csv() (in module biom3d.preprocess) generate_train_batch() (biom3d.datasets.semseg_batchgen.BatchGenDataLoader method) get() (biom3d.utils.DataHandlerFactory static method) (biom3d.utils.time.Time method) get_activation() (biom3d.models.unet3d_eff.EffUNet method) get_aug_patch() (in module biom3d.auto_config) get_bbox() (in module biom3d.datasets.semseg_batchgen) get_folds_df() (in module biom3d.utils.fold) get_folds_train_test_df() (in module biom3d.utils.fold) get_gridsampler() (biom3d.predictors.LoadImgPatch method) get_image_size() (biom3d.models.encoder_efficientnet3d.EfficientNet3D class method) get_indices() (biom3d.datasets.semseg_batchgen.BatchGenDataLoader method) get_last_lr() (biom3d.callbacks.LRSchedulerCosine method) (biom3d.callbacks.LRSchedulerMultiStep method) get_layer() (in module biom3d.models.unet3d_eff)

get_model_params() (in module biom3d.models.encoder_efficientnet3d) get_outfmaps() (in module biom3d.models.unet3d_eff) get_output() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) get_patch_size() (in module biom3d.datasets.semseg_batchgen) get_pyramid() (in module biom3d.models.unet3d_eff) get_resample_shape() (in module biom3d.preprocess) get_splits_train_val_test() (in module biom3d.utils.fold) get_splits_train_val_test_overlapping() (in module biom3d.utils.fold) get_tp_fp_fn_tn() (in module biom3d.metrics) get_train_test_df() (in module biom3d.utils.fold) get_training_transforms() (in module biom3d.datasets.semseg_batchgen) get_validation_transforms() (in module biom3d.datasets.semseg_batchgen) global_crop_resize() (biom3d.utils.data_augmentation.SmartPatch method) GlobalAvgPool3d (class in biom3d.models.encoder_vgg) GlobalParams() (in module biom3d.models.encoder_efficientnet3d) GlobalScaleScheduler (class in biom3d.callbacks)

H

hold_out() (in module biom3d.preprocess)

I

ImageManager (class in biom3d.utils.data_handler.file_handler) images (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) ImageSaver (class in biom3d.callbacks)

IMG (biom3d.utils.data_handler.data_handler_abstract.OutputType attribute) imread() (in module biom3d.datasets.semseg_batchgen) insert_prefix_to_name() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) IoU (class in biom3d.metrics)

K

keep_big_volumes() (in module biom3d.utils.filtering)

keep_biggest_volume_centered() (in module biom3d.utils.filtering) keep_center_only() (in module biom3d.utils.filtering)

L

LabelToBool (class in biom3d.datasets.semseg_torchio) LabelToFloat (class in biom3d.datasets.semseg_torchio) LabelToLong (class in biom3d.datasets.semseg_patch_fast) (class in biom3d.datasets.semseg_torchio) LambdaLayer (class in biom3d.models.encoder_vgg) load() (biom3d.models.unet3d_vgg_deep.UNet method) (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) load_img_seg() (in module biom3d.predictors) load_python_config() (in module biom3d.utils.config) load_yaml_config() (in module biom3d.utils.config)

LoadImgPatch (class in biom3d.predictors) local_crop_pad() (biom3d.utils.data_augmentation.SmartPatch method) local_crop_resize() (biom3d.utils.data_augmentation.SmartPatch method) located_crop() (in module biom3d.datasets.semseg_batchgen) (in module biom3d.datasets.semseg_patch_fast) LogPrinter (class in biom3d.callbacks) LogSaver (class in biom3d.callbacks) LRSchedulerCosine (class in biom3d.callbacks) LRSchedulerMultiStep (class in biom3d.callbacks) LRSchedulerPoly (class in biom3d.callbacks)

M

main() (in module biom3d.omero_downloader) main_pretrain_seg_pred_eval() (in module biom3d.train) main_seg_pred_eval() (in module biom3d.train) masks (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) MBConvBlock3D (class in biom3d.models.encoder_efficientnet3d) MemoryEfficientSwish (class in biom3d.models.encoder_efficientnet3d) Metric (class in biom3d.metrics) MetricsUpdater (class in biom3d.callbacks) ModelSaver (class in biom3d.callbacks) module biom3d.auto_config biom3d.callbacks biom3d.datasets.semseg_batchgen biom3d.datasets.semseg_patch_fast biom3d.datasets.semseg_torchio biom3d.eval biom3d.metrics biom3d.models.decoder_vgg_deep biom3d.models.encoder_efficientnet3d biom3d.models.encoder_vgg biom3d.models.unet3d_eff biom3d.models.unet3d_vgg_deep biom3d.omero_downloader biom3d.omero_pred biom3d.pred biom3d.predictors biom3d.preprocess biom3d.preprocess_train biom3d.train biom3d.trainers biom3d.utils.config biom3d.utils.data_augmentation biom3d.utils.decorators biom3d.utils.encoding biom3d.utils.filtering biom3d.utils.fold biom3d.utils.image biom3d.utils.neural_network biom3d.utils.os biom3d.utils.time

MomentumScheduler (class in biom3d.callbacks) MSE (class in biom3d.metrics) MSK (biom3d.utils.data_handler.data_handler_abstract.OutputType attribute) msk_outpath (biom3d.utils.data_handler.data_handler_abstract.DataHandler attribute) MTBatchGenDataLoader (class in biom3d.datasets.semseg_batchgen)

N

napari_viewer() (in module biom3d.utils.image) nested_dict_change_value() (in module biom3d.utils.config)

nested_dict_change_value_case_insensitive() (in module biom3d.utils.config) nested_dict_pairs_iterator() (in module biom3d.utils.config) nnUNetRandomCropAndPadTransform (class in biom3d.datasets.semseg_batchgen)

O

OBJ_INFO (in module biom3d.omero_downloader) on_batch_begin() (biom3d.callbacks.Callback method) (biom3d.callbacks.Callbacks method) on_batch_end() (biom3d.callbacks.Callback method) (biom3d.callbacks.Callbacks method) (biom3d.callbacks.LogPrinter method) (biom3d.callbacks.MetricsUpdater method) on_epoch_begin() (biom3d.callbacks.Callback method) (biom3d.callbacks.Callbacks method) (biom3d.callbacks.DatasetSizeScheduler method) (biom3d.callbacks.ForceFGScheduler method) (biom3d.callbacks.GlobalScaleScheduler method) (biom3d.callbacks.LogPrinter method) (biom3d.callbacks.LRSchedulerPoly method) (biom3d.callbacks.MetricsUpdater method) (biom3d.callbacks.OverlapScheduler method) (biom3d.callbacks.TensorboardSaver method) (biom3d.callbacks.WeightDecayScheduler method) on_epoch_end() (biom3d.callbacks.Callback method) (biom3d.callbacks.Callbacks method) (biom3d.callbacks.ImageSaver method) (biom3d.callbacks.LogSaver method) (biom3d.callbacks.LRSchedulerCosine method) (biom3d.callbacks.LRSchedulerMultiStep method) (biom3d.callbacks.ModelSaver method) (biom3d.callbacks.MomentumScheduler method) (biom3d.callbacks.TensorboardSaver method)

on_train_begin() (biom3d.callbacks.Callback method) (biom3d.callbacks.Callbacks method) (biom3d.callbacks.ModelSaver method) on_train_end() (biom3d.callbacks.Callback method) (biom3d.callbacks.Callbacks method) one_hot() (in module biom3d.utils.encoding) one_hot_fast() (in module biom3d.utils.encoding) one_hot_fast_v1() (in module biom3d.utils.encoding) open() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) otsu_thresholding() (in module biom3d.utils.filtering) OutputType (class in biom3d.utils.data_handler.data_handler_abstract) OverlapScheduler (class in biom3d.callbacks)

P

parameters_return() (in module biom3d.auto_config) post_process() (biom3d.predictors.LoadImgPatch method) PRED (biom3d.utils.data_handler.data_handler_abstract.OutputType attribute) pred() (in module biom3d.pred) pred_multiple() (in module biom3d.pred)

pred_seg() (in module biom3d.pred) pred_seg_eval() (in module biom3d.pred) pred_seg_eval_single() (in module biom3d.pred) pred_single() (in module biom3d.pred) preprocess_train() (in module biom3d.preprocess_train) Preprocessing (class in biom3d.preprocess)

R

random_crop() (in module biom3d.datasets.semseg_batchgen) (in module biom3d.datasets.semseg_patch_fast) random_crop_pad() (in module biom3d.datasets.semseg_batchgen) (in module biom3d.datasets.semseg_patch_fast) random_crop_resize() (in module biom3d.datasets.semseg_patch_fast) RandomCropAndPadTransform (class in biom3d.datasets.semseg_batchgen) RandomCropOrPad (class in biom3d.datasets.semseg_torchio) recursive_rename_key() (in module biom3d.utils.config) replace_line_multiple() (in module biom3d.utils.config) replace_line_single() (in module biom3d.utils.config) reset() (biom3d.datasets.semseg_batchgen.BatchGenDataLoader method) (biom3d.metrics.Metric method) (biom3d.utils.time.Time method)

reset_iterator() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) resize_3d() (in module biom3d.utils.image) resize_img_msk() (in module biom3d.preprocess) resize_segmentation() (in module biom3d.utils.image) robust_sort() (in module biom3d.eval) RobustCrossEntropyLoss (class in biom3d.metrics) round_filters() (in module biom3d.models.encoder_efficientnet3d) round_repeats() (in module biom3d.models.encoder_efficientnet3d) run() (biom3d.preprocess.Preprocessing method) (in module biom3d.omero_pred)

S

sanity_check() (in module biom3d.preprocess) save() (biom3d.utils.data_handler.data_handler_abstract.DataHandler method) save_python_config() (in module biom3d.utils.config) save_yaml_config() (in module biom3d.utils.config) seg_patch_train() (in module biom3d.trainers) seg_patch_validate() (in module biom3d.trainers) seg_postprocessing() (in module biom3d.predictors) seg_predict() (in module biom3d.predictors) seg_predict_old() (in module biom3d.predictors) seg_predict_patch() (in module biom3d.predictors) seg_predict_patch_2() (in module biom3d.predictors) seg_preprocessor() (in module biom3d.preprocess) seg_train() (in module biom3d.trainers) seg_validate() (in module biom3d.trainers)

SemSeg3DPatchFast (class in biom3d.datasets.semseg_patch_fast) set_fg_rate() (biom3d.datasets.semseg_patch_fast.SemSeg3DPatchFast method) set_swish() (biom3d.models.encoder_efficientnet3d.EfficientNet3D method) (biom3d.models.encoder_efficientnet3d.MBConvBlock3D method) set_trainer() (biom3d.callbacks.Callback method) (biom3d.callbacks.Callbacks method) SmallEncoderBlock (class in biom3d.models.encoder_vgg) SmartPatch (class in biom3d.utils.data_augmentation) SoftDiceLoss (class in biom3d.metrics) standardize_img_dims() (in module biom3d.preprocess) str() (biom3d.metrics.Metric method) strat_kfold() (in module biom3d.preprocess) sum_tensor() (in module biom3d.metrics) Swish (class in biom3d.models.encoder_efficientnet3d) SwishImplementation (class in biom3d.models.encoder_efficientnet3d)

T

TensorboardSaver (class in biom3d.callbacks) Time (class in biom3d.utils.time)

TorchioDataset (class in biom3d.datasets.semseg_torchio) TorchIOReaderWrapper (class in biom3d.datasets.semseg_torchio) train() (in module biom3d.train)

U

UNet (class in biom3d.models.unet3d_vgg_deep) unfreeze_encoder() (biom3d.models.unet3d_eff.EffUNet method) (biom3d.models.unet3d_vgg_deep.UNet method)

update() (biom3d.metrics.Metric method)

V

VGGDecoder (class in biom3d.models.decoder_vgg_deep)

VGGEncoder (class in biom3d.models.encoder_vgg) volumes() (in module biom3d.utils.filtering)

W

WeightDecayScheduler (class in biom3d.callbacks)

write_file_head() (biom3d.callbacks.LogSaver method)