Index

A

adapt_bmz_model_kwargs() (in module biapy.models) add_gaussian_noise() (in module biapy.data.pre_processing) add_meter() (biapy.utils.misc.MetricLogger method) adjust_learning_rate() (biapy.engine.schedulers.warmup_cosine_decay.WarmUpCosineDecayScheduler method) after_all_chunk_prediction_workflow_process() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method) after_all_chunk_prediction_workflow_process_master_rank() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method) after_all_images() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method) after_full_image() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method)

after_merge_patches() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method) after_one_chunk_raw_prediction() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) after_one_chunk_workflow_process() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) all_reduce_mean() (in module biapy.utils.misc) apply_binary_mask() (in module biapy.data.post_processing.post_processing) apply_clahe() (in module biapy.data.pre_processing) apply_gaussian_blur() (in module biapy.data.pre_processing) apply_histogram_matching() (in module biapy.data.pre_processing) apply_label_refinement() (in module biapy.data.post_processing.post_processing) apply_median_blur() (in module biapy.data.pre_processing) apply_median_filtering() (in module biapy.data.post_processing.post_processing) apply_model_activations() (biapy.engine.base_workflow.Base_Workflow method) apply_post_processing() (in module biapy.data.post_processing) apply_structN2Vmask() (in module biapy.engine.denoising) apply_structN2Vmask3D() (in module biapy.engine.denoising) apply_transform() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method) (biapy.data.generators.pair_data_3D_generator.Pair3DImageDataGenerator method) (biapy.data.generators.single_base_data_generator.SingleBaseDataGenerator method) (biapy.data.generators.single_data_3D_generator.Single3DImageDataGenerator method) Attention_U_Net (class in biapy.models.attention_unet) AttentionBlock (class in biapy.models.blocks) avg (biapy.utils.misc.SmoothedValue property)

B

Base_Workflow (class in biapy.engine.base_workflow) biapy.config module biapy.config.config module biapy.data module biapy.data.data_2D_manipulation module biapy.data.data_3D_manipulation module biapy.data.data_manipulation module biapy.data.dataset module biapy.data.generators module biapy.data.generators.augmentors module biapy.data.generators.pair_base_data_generator module biapy.data.generators.pair_data_2D_generator module biapy.data.generators.pair_data_3D_generator module biapy.data.generators.single_base_data_generator module biapy.data.generators.single_data_2D_generator module biapy.data.generators.single_data_3D_generator module biapy.data.norm module biapy.data.post_processing module biapy.data.post_processing.post_processing module biapy.data.pre_processing module biapy.engine module biapy.engine.base_workflow module biapy.engine.check_configuration module biapy.engine.classification module biapy.engine.denoising module biapy.engine.detection module biapy.engine.instance_seg module biapy.engine.metrics module biapy.engine.schedulers module biapy.engine.schedulers.warmup_cosine_decay module biapy.engine.self_supervised module biapy.engine.semantic_seg module biapy.engine.super_resolution module biapy.engine.train_engine module

biapy.models module biapy.models.attention_unet module biapy.models.blocks module biapy.models.bmz_utils module biapy.models.dfcan module biapy.models.edsr module biapy.models.efficientnet module biapy.models.hrnet module biapy.models.mae module biapy.models.memory_bank module biapy.models.multiresunet module biapy.models.rcan module biapy.models.resunet module biapy.models.resunet_plus_plus module biapy.models.resunet_se module biapy.models.seunet module biapy.models.simple_cnn module biapy.models.tr_layers module biapy.models.unet module biapy.models.unetr module biapy.models.unext_v1 module biapy.models.unext_v2 module biapy.models.vit module biapy.models.wdsr module biapy.utils module biapy.utils.callbacks module biapy.utils.misc module biapy.utils.util module BiaPyDataset (class in biapy.data.dataset) Block (class in biapy.models.wdsr) bmz_model_call() (biapy.engine.base_workflow.Base_Workflow method) brightness() (in module biapy.data.generators.augmentors) build_bmz_model() (in module biapy.models) build_callbacks() (in module biapy.engine) build_model() (in module biapy.models) build_torchvision_model() (in module biapy.models) by_chunks_collate_fn() (in module biapy.data.generators) by_chunks_workflow_collate_fn() (in module biapy.data.generators)

C

calculate_synapse_det_metrics_on_points() (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) calculate_volume_prob_map() (in module biapy.data.pre_processing) can_import_env_deps() (in module biapy.models) center_crop_single() (in module biapy.data.generators.augmentors) ChannelAttention (class in biapy.models.rcan) check_bmz_args() (in module biapy.models) check_bmz_model_compatibility() (in module biapy.models) check_configuration() (in module biapy.engine.check_configuration) check_downsample_division() (in module biapy.utils.util) check_generator_consistence() (in module biapy.data.generators) check_masks() (in module biapy.data.data_manipulation) check_value() (in module biapy.data.data_manipulation) Classification_Workflow (class in biapy.engine.classification) clean_dataset() (biapy.data.dataset.BiaPyDataset method) collect_point_type_csv_files() (in module biapy.data.post_processing.post_processing) compute_threads_and_workers() (in module biapy.utils.misc) Config (class in biapy.config.config) connect_pre_post_synapse_points_by_distance() (in module biapy.data.post_processing.post_processing) contrast() (in module biapy.data.generators.augmentors) ContrastCELoss (class in biapy.engine.metrics) Conv_batchnorm (class in biapy.models.multiresunet) ConvBlock (class in biapy.models.blocks) convert_old_model_cfg_to_current_version() (in module biapy.engine.check_configuration) ConvNeXtBlock_V1 (class in biapy.models.blocks) ConvNeXtBlock_V2 (class in biapy.models.blocks) copy() (biapy.config.config.Config method) (biapy.data.dataset.BiaPyDataset method) (biapy.data.dataset.DataSample method) (biapy.data.dataset.DatasetFile method) (biapy.data.dataset.PatchCoords method)

crappify() (in module biapy.data.pre_processing) create_chunked_test_generator() (in module biapy.data.generators) create_chunked_workflow_process_generator() (in module biapy.data.generators) create_detection_masks() (in module biapy.data.pre_processing) create_environment_file_for_model() (in module biapy.models.bmz_utils) create_file_sha256sum() (in module biapy.utils.util) create_HoVe_channels() (in module biapy.data.pre_processing) create_instance_channels() (in module biapy.data.pre_processing) create_instances() (biapy.data.post_processing.post_processing.Embedding_cluster method) create_model_cover() (in module biapy.models.bmz_utils) create_model_doc() (in module biapy.models.bmz_utils) create_plots() (in module biapy.utils.util) create_ssl_source_data_masks() (in module biapy.data.pre_processing) create_synapses_from_point_probs() (in module biapy.data.post_processing.post_processing) create_test_generator() (in module biapy.data.generators) create_th_plot() (in module biapy.data.post_processing.post_processing) create_train_val_augmentors() (in module biapy.data.generators) crop_3D_data_with_overlap() (in module biapy.data.data_3D_manipulation) crop_data_with_overlap() (in module biapy.data.data_2D_manipulation) CrossEntropyLoss_wrapper (class in biapy.engine.metrics) cutblur() (in module biapy.data.generators.augmentors) cutmix() (in module biapy.data.generators.augmentors) cutnoise() (in module biapy.data.generators.augmentors) cutout() (in module biapy.data.generators.augmentors)

D

data_range() (in module biapy.data.data_manipulation) DataSample (class in biapy.data.dataset) DatasetFile (class in biapy.data.dataset) decide_dtype() (in module biapy.data.data_manipulation) define_activations_and_channels() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method) define_metrics() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method)

Denoising_Workflow (class in biapy.engine.denoising) dequeue_and_enqueue() (biapy.models.memory_bank.MemoryBank method) destroy_test_data() (biapy.engine.base_workflow.Base_Workflow method) destroy_train_data() (biapy.engine.base_workflow.Base_Workflow method) detect_edges() (in module biapy.data.pre_processing) detection_loss (class in biapy.engine.metrics) detection_metrics() (in module biapy.engine.metrics) detection_process() (biapy.engine.detection.Detection_Workflow method) detection_watershed() (in module biapy.data.post_processing.post_processing) Detection_Workflow (class in biapy.engine.detection) DFCAN (class in biapy.models.dfcan) DiceCELoss (class in biapy.engine.metrics) DiceLoss (class in biapy.engine.metrics) diff_between_configs() (in module biapy.engine.check_configuration) divide_images_on_classes() (in module biapy.utils.util) do_save_wm() (in module biapy.utils.util) DoubleConvBlock (class in biapy.models.blocks) download_to_local_path() (in module biapy.models.bmz_utils) draw_grid() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method) (biapy.data.generators.single_base_data_generator.SingleBaseDataGenerator method) dropout() (in module biapy.data.generators.augmentors)

E

EarlyStopping (class in biapy.utils.callbacks) EDSR (class in biapy.models.edsr) efficientnet() (in module biapy.models.efficientnet) elastic() (in module biapy.data.generators.augmentors) Embedding_cluster (class in biapy.data.post_processing.post_processing) ensemble16_3d_predictions() (in module biapy.data.post_processing.post_processing) ensemble8_2d_predictions() (in module biapy.data.post_processing.post_processing) ensure_2d_shape() (in module biapy.data.data_2D_manipulation) ensure_3d_shape() (in module biapy.data.data_3D_manipulation) euler_integration() (in module biapy.data.pre_processing) evaluate() (in module biapy.engine.train_engine)

expansion (biapy.models.blocks.HRBasicBlock attribute) (biapy.models.blocks.HRBottleneck attribute) extract_3D_patch_with_overlap_and_padding_yield() (in module biapy.data.data_3D_manipulation) extract_BMZ_sample_and_cover() (in module biapy.models.bmz_utils) extract_model() (in module biapy.models) extract_patch_from_efficient_file() (in module biapy.data.data_3D_manipulation) extract_patch_within_image() (in module biapy.data.data_manipulation) extract_points_in_predictions() (in module biapy.data.post_processing.post_processing) extract_shape_from_coords() (biapy.data.dataset.PatchCoords method) extract_synapse_connectivity() (in module biapy.data.post_processing.post_processing) extract_synful_synapses() (in module biapy.data.post_processing.post_processing)

F

fftshift2d() (in module biapy.models.dfcan) fftshift3d() (in module biapy.models.dfcan) fill_label_holes() (in module biapy.data.post_processing.post_processing) filter_samples_by_properties() (in module biapy.data.data_manipulation) find_bmz_models() (in module biapy.models) find_closest_key() (in module biapy.data.post_processing.post_processing) find_neighbors() (in module biapy.data.post_processing.post_processing) flip_horizontal() (in module biapy.data.generators.augmentors) flip_vertical() (in module biapy.data.generators.augmentors) flush() (biapy.utils.misc.TensorboardLogger method) foreground_percentage() (in module biapy.utils.util) forward() (biapy.engine.metrics.ContrastCELoss method) (biapy.engine.metrics.DiceCELoss method) (biapy.engine.metrics.DiceLoss method) (biapy.engine.metrics.loss_encapsulation method) (biapy.engine.metrics.PixelContrastLoss method) (biapy.engine.metrics.SpatialEmbLoss method) (biapy.engine.metrics.SSIM_loss method) (biapy.engine.metrics.W_MAE_SSIM_loss method) (biapy.engine.metrics.W_MSE_SSIM_loss method) (biapy.models.attention_unet.Attention_U_Net method) (biapy.models.blocks.AttentionBlock method) (biapy.models.blocks.ConvBlock method) (biapy.models.blocks.ConvNeXtBlock_V1 method) (biapy.models.blocks.ConvNeXtBlock_V2 method) (biapy.models.blocks.DoubleConvBlock method) (biapy.models.blocks.GRN method) (biapy.models.blocks.HRBasicBlock method) (biapy.models.blocks.HRBottleneck method) (biapy.models.blocks.ResConvBlock method) (biapy.models.blocks.ResUNetPlusPlus_AttentionBlock method) (biapy.models.blocks.ResUpBlock method) (biapy.models.blocks.SqExBlock method) (biapy.models.blocks.UpBlock method) (biapy.models.blocks.UpConvNeXtBlock_V1 method) (biapy.models.blocks.UpConvNeXtBlock_V2 method) (biapy.models.dfcan.DFCAN method) (biapy.models.dfcan.RCAB method) (biapy.models.dfcan.ResGroup method) (biapy.models.edsr.EDSR method) (biapy.models.edsr.SR_convblock method) (biapy.models.edsr.SR_upsampling method) (biapy.models.hrnet.HighResolutionModule method) (biapy.models.hrnet.HighResolutionNet method) (biapy.models.mae.MaskedAutoencoderViT method) (biapy.models.multiresunet.Conv_batchnorm method) (biapy.models.multiresunet.Multiresblock method) (biapy.models.multiresunet.MultiResUnet method) (biapy.models.multiresunet.Respath method) (biapy.models.rcan.ChannelAttention method) (biapy.models.rcan.RCAB method) (biapy.models.rcan.rcan method) (biapy.models.rcan.RG method) (biapy.models.resunet.ResUNet method) (biapy.models.resunet_plus_plus.ResUNetPlusPlus method) (biapy.models.resunet_se.ResUNet_SE method) (biapy.models.seunet.SE_U_Net method) (biapy.models.simple_cnn.simple_CNN method) (biapy.models.tr_layers.PatchEmbed method) (biapy.models.unet.U_Net method) (biapy.models.unetr.UNETR method) (biapy.models.unext_v1.U_NeXt_V1 method) (biapy.models.unext_v2.U_NeXt_V2 method) (biapy.models.vit.VisionTransformer method) (biapy.models.wdsr.Block method) (biapy.models.wdsr.wdsr method)

forward_decoder() (biapy.models.mae.MaskedAutoencoderViT method) forward_encoder() (biapy.models.mae.MaskedAutoencoderViT method) forward_features() (biapy.models.vit.VisionTransformer method) forward_loss() (biapy.models.mae.MaskedAutoencoderViT method)

G

gamma_contrast() (in module biapy.data.generators.augmentors) gaussian_blur() (in module biapy.data.generators.augmentors) generate_ellipse_footprint() (in module biapy.data.pre_processing) generate_rays() (in module biapy.data.pre_processing) get_activation() (in module biapy.models.blocks) get_bmz_model_info() (in module biapy.models.bmz_utils) get_bmz_model_kwargs() (in module biapy.models) get_cfg_defaults() (biapy.config.config.Config method) get_cfg_key_value() (in module biapy.utils.util) get_checkpoint_path() (in module biapy.utils.misc) get_class_num() (biapy.data.dataset.DatasetFile method) get_grad_norm_() (in module biapy.utils.misc) get_gt_associated_id() (biapy.data.dataset.DataSample method) get_input_axes() (biapy.data.dataset.DatasetFile method) get_last_layer_info() (in module biapy.models) get_norm_2d() (in module biapy.models.blocks) get_norm_3d() (in module biapy.models.blocks)

get_num_inchannels() (biapy.models.hrnet.HighResolutionModule method) get_path_in_zarr() (biapy.data.dataset.DataSample method) get_rank() (in module biapy.utils.misc) get_shape() (biapy.data.dataset.DataSample method) get_stratified_coords2D() (in module biapy.engine.denoising) get_stratified_coords3D() (in module biapy.engine.denoising) get_subpatch() (in module biapy.engine.denoising) get_transformed_samples() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method) (biapy.data.generators.single_base_data_generator.SingleBaseDataGenerator method) get_value_manipulation() (in module biapy.engine.denoising) get_world_size() (in module biapy.utils.misc) getitem() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method) (biapy.data.generators.single_base_data_generator.SingleBaseDataGenerator method) global_avg (biapy.utils.misc.SmoothedValue property) grayscale() (in module biapy.data.generators.augmentors) grid_masking() (biapy.models.mae.MaskedAutoencoderViT method) GridMask() (in module biapy.data.generators.augmentors) GRN (class in biapy.models.blocks)

H

HighResolutionModule (class in biapy.models.hrnet) HighResolutionNet (class in biapy.models.hrnet)

HRBasicBlock (class in biapy.models.blocks) HRBottleneck (class in biapy.models.blocks)

I

im2col() (in module biapy.utils.util) img_is_loaded() (biapy.data.dataset.DataSample method) img_to_onehot_encoding() (in module biapy.data.data_manipulation) imread() (in module biapy.data.data_manipulation) imwrite() (in module biapy.data.data_manipulation) init_devices() (in module biapy.utils.misc) init_embedding_output() (in module biapy.models) init_weights() (in module biapy.models.blocks)

initialize_weights() (biapy.models.mae.MaskedAutoencoderViT method) insert_patch_in_efficient_file() (in module biapy.data.data_3D_manipulation) instance_seg_process() (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) instance_segmentation_loss (class in biapy.engine.metrics) Instance_Segmentation_Workflow (class in biapy.engine.instance_seg) is_biapy_model() (in module biapy.models) is_dist_avail_and_initialized() (in module biapy.utils.misc) is_main_process() (in module biapy.utils.misc) is_parallel() (biapy.data.dataset.DatasetFile method)

J

jaccard_index (class in biapy.engine.metrics)

jaccard_index_numpy() (in module biapy.engine.metrics) jaccard_index_numpy_without_background() (in module biapy.engine.metrics)

L

labels_into_channels() (in module biapy.data.pre_processing) load_3D_efficient_files() (in module biapy.data.data_3D_manipulation) load_and_prepare_cls_test_data() (in module biapy.data.data_manipulation) load_and_prepare_test_data() (in module biapy.data.data_manipulation) load_and_prepare_train_data() (in module biapy.data.data_manipulation) load_and_prepare_train_data_cls() (in module biapy.data.data_manipulation) load_cls_data_from_dir() (in module biapy.data.data_manipulation) load_data_from_dir() (in module biapy.data.data_manipulation) load_images_to_dataset() (in module biapy.data.data_manipulation) load_img_data() (in module biapy.data.data_manipulation) load_img_part_from_efficient_file() (in module biapy.data.data_3D_manipulation)

load_model_checkpoint() (in module biapy.utils.misc) load_sample() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method) (biapy.data.generators.single_base_data_generator.SingleBaseDataGenerator method) load_synapse_gt_points() (in module biapy.data.data_3D_manipulation) load_test_data() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) load_train_data() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) log_every() (biapy.utils.misc.MetricLogger method) looks_like_hdf5() (in module biapy.data.data_3D_manipulation) loss_encapsulation (class in biapy.engine.metrics) lovasz_hinge() (in module biapy.engine.metrics)

M

mae_vit_base_patch16() (in module biapy.models.mae) mae_vit_base_patch16_dec512d8b() (in module biapy.models.mae) mae_vit_huge_patch14() (in module biapy.models.mae) mae_vit_huge_patch14_dec512d8b() (in module biapy.models.mae) mae_vit_large_patch16() (in module biapy.models.mae) mae_vit_large_patch16_dec512d8b() (in module biapy.models.mae) make_weight_map() (in module biapy.utils.util) manipulate_val_data() (in module biapy.engine.denoising) mask_center() (in module biapy.engine.denoising) MaskedAutoencoderViT (class in biapy.models.mae) MaskedAutoencoderViT_loss_wrapper() (biapy.engine.self_supervised.Self_supervised_Workflow method) max (biapy.utils.misc.SmoothedValue property) measure_morphological_props_and_filter() (in module biapy.data.post_processing.post_processing) median (biapy.utils.misc.SmoothedValue property) median_blur() (in module biapy.data.generators.augmentors) MemoryBank (class in biapy.models.memory_bank) merge_3D_data_with_overlap() (in module biapy.data.data_3D_manipulation) merge_data_with_overlap() (in module biapy.data.data_2D_manipulation) merge_import_lines() (in module biapy.models) metric_calculation() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method) MetricLogger (class in biapy.utils.misc) misalignment() (in module biapy.data.generators.augmentors) missing_sections() (in module biapy.data.generators.augmentors) model_call_func() (biapy.engine.base_workflow.Base_Workflow method) module biapy.config biapy.config.config biapy.data biapy.data.data_2D_manipulation biapy.data.data_3D_manipulation biapy.data.data_manipulation biapy.data.dataset biapy.data.generators biapy.data.generators.augmentors biapy.data.generators.pair_base_data_generator biapy.data.generators.pair_data_2D_generator biapy.data.generators.pair_data_3D_generator biapy.data.generators.single_base_data_generator biapy.data.generators.single_data_2D_generator biapy.data.generators.single_data_3D_generator biapy.data.norm biapy.data.post_processing biapy.data.post_processing.post_processing biapy.data.pre_processing biapy.engine biapy.engine.base_workflow biapy.engine.check_configuration biapy.engine.classification biapy.engine.denoising biapy.engine.detection biapy.engine.instance_seg biapy.engine.metrics biapy.engine.schedulers biapy.engine.schedulers.warmup_cosine_decay biapy.engine.self_supervised biapy.engine.semantic_seg biapy.engine.super_resolution biapy.engine.train_engine biapy.models biapy.models.attention_unet biapy.models.blocks biapy.models.bmz_utils biapy.models.dfcan biapy.models.edsr biapy.models.efficientnet biapy.models.hrnet biapy.models.mae biapy.models.memory_bank biapy.models.multiresunet biapy.models.rcan biapy.models.resunet biapy.models.resunet_plus_plus biapy.models.resunet_se biapy.models.seunet biapy.models.simple_cnn biapy.models.tr_layers biapy.models.unet biapy.models.unetr biapy.models.unext_v1 biapy.models.unext_v2 biapy.models.vit biapy.models.wdsr biapy.utils biapy.utils.callbacks biapy.utils.misc biapy.utils.util

motion_blur() (in module biapy.data.generators.augmentors) multiple_metrics (class in biapy.engine.metrics) Multiresblock (class in biapy.models.multiresunet) MultiResUnet (class in biapy.models.multiresunet)

N

n2v_loss_mse() (in module biapy.engine.metrics) norm_channel() (in module biapy.data.pre_processing) norm_range01() (in module biapy.data.norm) normal_int() (in module biapy.engine.denoising)

normalize_image() (in module biapy.data.norm) normalize_mask() (in module biapy.data.norm) normalize_stats() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method)

O

onehot_encoding_to_img() (in module biapy.data.data_manipulation)

order_dimensions() (in module biapy.data.data_3D_manipulation) os_walk_clean() (in module biapy.utils.misc)

P

pad_and_reflect() (in module biapy.data.data_manipulation) Pair2DImageDataGenerator (class in biapy.data.generators.pair_data_2D_generator) Pair3DImageDataGenerator (class in biapy.data.generators.pair_data_3D_generator) PairBaseDataGenerator (class in biapy.data.generators.pair_base_data_generator) PatchCoords (class in biapy.data.dataset) PatchEmbed (class in biapy.models.tr_layers) patchify() (biapy.models.mae.MaskedAutoencoderViT method) percentile_clip() (in module biapy.data.norm) pick_chunks() (in module biapy.data.data_3D_manipulation) PixelContrastLoss (class in biapy.engine.metrics) pm_identity() (in module biapy.engine.denoising) pm_mean() (in module biapy.engine.denoising) pm_median() (in module biapy.engine.denoising) pm_normal_additive() (in module biapy.engine.denoising) pm_normal_fitted() (in module biapy.engine.denoising) pm_normal_withoutCP() (in module biapy.engine.denoising) pm_uniform_withCP() (in module biapy.engine.denoising) pm_uniform_withoutCP() (in module biapy.engine.denoising) predict_batches_in_test() (biapy.engine.base_workflow.Base_Workflow method) prepare_activation_layers() (in module biapy.models.blocks) prepare_bmz_data() (biapy.engine.base_workflow.Base_Workflow method) prepare_detection_data() (biapy.engine.detection.Detection_Workflow method) prepare_instance_data() (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) prepare_logging_tool() (biapy.engine.base_workflow.Base_Workflow method)

prepare_model() (biapy.engine.base_workflow.Base_Workflow method) prepare_n2v() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method) prepare_optimizer() (in module biapy.engine) prepare_ssl_data() (biapy.engine.self_supervised.Self_supervised_Workflow method) prepare_targets() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) prepare_test_generators() (biapy.engine.base_workflow.Base_Workflow method) prepare_train_generators() (biapy.engine.base_workflow.Base_Workflow method) preprocess_data() (in module biapy.data.pre_processing) print_stats() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) process_test_sample() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method) process_test_sample_by_chunks() (biapy.engine.base_workflow.Base_Workflow method) proj_feat() (biapy.models.unetr.UNETR method)

R

radial_distances() (in module biapy.data.pre_processing) random_3D_crop_pair() (in module biapy.data.generators.augmentors) random_3D_crop_single() (in module biapy.data.generators.augmentors) random_crop_pair() (in module biapy.data.generators.augmentors) random_crop_single() (in module biapy.data.generators.augmentors) random_masking() (biapy.models.mae.MaskedAutoencoderViT method) random_neighbor() (in module biapy.engine.denoising) RCAB (class in biapy.models.dfcan) (class in biapy.models.rcan) rcan (class in biapy.models.rcan) read_chunked_data() (in module biapy.data.data_3D_manipulation) read_chunked_nested_data() (in module biapy.data.data_3D_manipulation) read_chunked_nested_h5() (in module biapy.data.data_3D_manipulation) read_chunked_nested_zarr() (in module biapy.data.data_3D_manipulation) read_img_as_ndarray() (in module biapy.data.data_manipulation) reduce_dtype() (in module biapy.data.data_manipulation)

remove_close_points() (in module biapy.data.post_processing.post_processing) remove_close_points_by_mask() (in module biapy.data.post_processing.post_processing) repare_large_blobs() (in module biapy.data.post_processing.post_processing) ResConvBlock (class in biapy.models.blocks) ResGroup (class in biapy.models.dfcan) resize() (in module biapy.data.data_manipulation) resize_images() (in module biapy.data.pre_processing) resize_img() (in module biapy.data.generators.augmentors) resolve_cpu_budget() (in module biapy.utils.misc) Respath (class in biapy.models.multiresunet) ResUNet (class in biapy.models.resunet) ResUNet_SE (class in biapy.models.resunet_se) ResUNetPlusPlus (class in biapy.models.resunet_plus_plus) ResUNetPlusPlus_AttentionBlock (class in biapy.models.blocks) ResUpBlock (class in biapy.models.blocks) RG (class in biapy.models.rcan) rotation() (in module biapy.data.generators.augmentors)

S

sample_coords() (in module biapy.engine.denoising) sample_satisfy_conds() (in module biapy.data.data_manipulation) samples_from_class_list() (in module biapy.data.data_manipulation) samples_from_image_list() (in module biapy.data.data_manipulation) samples_from_image_list_multiple_raw_one_gt() (in module biapy.data.data_manipulation) samples_from_zarr() (in module biapy.data.data_manipulation) save_aug_samples() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method) (biapy.data.generators.pair_data_2D_generator.Pair2DImageDataGenerator method) (biapy.data.generators.pair_data_3D_generator.Pair3DImageDataGenerator method) (biapy.data.generators.single_base_data_generator.SingleBaseDataGenerator method) (biapy.data.generators.single_data_2D_generator.Single2DImageDataGenerator method) (biapy.data.generators.single_data_3D_generator.Single3DImageDataGenerator method) save_filters_of_convlayer() (in module biapy.utils.util) save_images() (biapy.models.mae.MaskedAutoencoderViT method) save_model() (in module biapy.utils.misc) save_npy_files() (in module biapy.data.data_manipulation) save_on_master() (in module biapy.utils.misc) save_tif() (in module biapy.data.data_manipulation) save_tif_pair_discard() (in module biapy.data.data_manipulation) scale_target() (in module biapy.engine.metrics) SE_U_Net (class in biapy.models.seunet) seg2aff_pni() (in module biapy.utils.util) seg_widen_border() (in module biapy.utils.util) Self_supervised_Workflow (class in biapy.engine.self_supervised)

Semantic_Segmentation_Workflow (class in biapy.engine.semantic_seg) set_seed() (in module biapy.utils.misc) set_step() (biapy.utils.misc.TensorboardLogger method) setup_for_distributed() (in module biapy.utils.misc) shape_mismatch_message() (in module biapy.data.data_manipulation) shear() (in module biapy.data.generators.augmentors) shift() (in module biapy.data.generators.augmentors) shuffle_channels() (in module biapy.data.generators.augmentors) simple_CNN (class in biapy.models.simple_cnn) Single2DImageDataGenerator (class in biapy.data.generators.single_data_2D_generator) Single3DImageDataGenerator (class in biapy.data.generators.single_data_3D_generator) SingleBaseDataGenerator (class in biapy.data.generators.single_base_data_generator) slice_from_props() (in module biapy.data.pre_processing) SmoothedValue (class in biapy.utils.misc) SpatialEmbLoss (class in biapy.engine.metrics) SqExBlock (class in biapy.models.blocks) SR_convblock (class in biapy.models.edsr) SR_upsampling (class in biapy.models.edsr) SSIM_loss (class in biapy.engine.metrics) SSIM_wrapper (class in biapy.engine.metrics) Super_resolution_Workflow (class in biapy.engine.super_resolution) synapse_channel_creation() (in module biapy.data.pre_processing) synapse_seg_process() (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) synchronize_between_processes() (biapy.utils.misc.MetricLogger method) (biapy.utils.misc.SmoothedValue method)

T

TensorboardLogger (class in biapy.utils.misc) test() (biapy.engine.base_workflow.Base_Workflow method) threshold_plots() (in module biapy.utils.util) time_text() (in module biapy.utils.misc) to_dict() (biapy.config.config.Config method) to_numpy_format() (in module biapy.utils.misc) to_pytorch_format() (in module biapy.utils.misc) torch_percentile() (in module biapy.data.norm) torchvision_model_call() (biapy.engine.base_workflow.Base_Workflow method) (biapy.engine.classification.Classification_Workflow method) (biapy.engine.denoising.Denoising_Workflow method) (biapy.engine.detection.Detection_Workflow method) (biapy.engine.instance_seg.Instance_Segmentation_Workflow method) (biapy.engine.self_supervised.Self_supervised_Workflow method) (biapy.engine.semantic_seg.Semantic_Segmentation_Workflow method) (biapy.engine.super_resolution.Super_resolution_Workflow method)

touching_mask_nd() (in module biapy.data.pre_processing) train() (biapy.engine.base_workflow.Base_Workflow method) train_one_epoch() (in module biapy.engine.train_engine)

U

U_Net (class in biapy.models.unet) U_NeXt_V1 (class in biapy.models.unext_v1) U_NeXt_V2 (class in biapy.models.unext_v2) undo_image_norm() (in module biapy.data.norm) undo_norm_range01() (in module biapy.data.norm) undo_zero_mean_unit_variance_normalization() (in module biapy.data.norm) unet_border_weight_map() (in module biapy.data.pre_processing) UNETR (class in biapy.models.unetr) unique_labels_fast() (in module biapy.data.pre_processing) unpatchify() (biapy.models.mae.MaskedAutoencoderViT method)

UpBlock (class in biapy.models.blocks) UpConvNeXtBlock_V1 (class in biapy.models.blocks) UpConvNeXtBlock_V2 (class in biapy.models.blocks) update() (biapy.utils.misc.MetricLogger method) (biapy.utils.misc.SmoothedValue method) (biapy.utils.misc.TensorboardLogger method) update_bmz_model_kwargs_to_biapy() (in module biapy.models) update_dependencies() (in module biapy.config.config) update_dict_with_existing_keys() (in module biapy.utils.misc) update_mask_norm_info() (in module biapy.data.norm)

V

value (biapy.utils.misc.SmoothedValue property) VisionTransformer (class in biapy.models.vit) vit_base_patch16() (in module biapy.models.vit)

vit_huge_patch14() (in module biapy.models.vit) vit_large_patch16() (in module biapy.models.vit) voronoi_on_mask() (in module biapy.data.post_processing.post_processing)

W

W_MAE_SSIM_loss (class in biapy.engine.metrics) W_MSE_SSIM_loss (class in biapy.engine.metrics) WarmUpCosineDecayScheduler (class in biapy.engine.schedulers.warmup_cosine_decay)

watershed_by_channels() (in module biapy.data.post_processing.post_processing) wdsr (class in biapy.models.wdsr) weight_binary_ratio() (in module biapy.engine.metrics)

Z

zero_mean_unit_variance_normalization() (in module biapy.data.norm)

zoom() (in module biapy.data.generators.augmentors)