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Semantic segmentation
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Semantic segmentation
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Detection
Denoising
Super-resolution
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classification
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utils
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BiaPy
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Index
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W
A
add_meter() (biapy.utils.misc.MetricLogger method)
adjust_learning_rate() (biapy.engine.schedulers.warmup_cosine_decay.WarmUpCosineDecayScheduler 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_merge_patches_by_chunks_proccess_entire_pred() (biapy.engine.base_workflow.Base_Workflow method)
after_merge_patches_by_chunks_proccess_patch() (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)
all_reduce_mean() (in module biapy.utils.misc)
apply_binary_mask() (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)
avg (biapy.utils.misc.SmoothedValue property)
B
Base_Workflow (class in biapy.engine.base_workflow)
bce_dice_loss() (in module biapy.engine.metrics)
biapy.config.config
module
biapy.data
module
biapy.data.data_2D_manipulation
module
biapy.data.data_3D_manipulation
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.post_processing
module
biapy.data.post_processing.post_processing
module
biapy.data.post_processing.smooth_tiled_predictions
module
biapy.engine
module
biapy.engine.base_workflow
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.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.dfcan
module
biapy.models.edsr
module
biapy.models.efficientnet
module
biapy.models.mae
module
biapy.models.multiresunet
module
biapy.models.rcan
module
biapy.models.resunet
module
biapy.models.seunet
module
biapy.models.simple_cnn
module
biapy.models.unet
module
biapy.models.unetr
module
biapy.models.vit
module
biapy.models.wdsr
module
biapy.utils.callbacks
module
biapy.utils.misc
module
biapy.utils.util
module
binary_crossentropy_weighted() (in module biapy.engine.metrics)
Block (class in biapy.models.wdsr)
bmz_model_call() (biapy.engine.base_workflow.Base_Workflow method)
boundary_refinement_watershed() (in module biapy.data.post_processing.post_processing)
boundary_refinement_watershed2() (in module biapy.data.post_processing.post_processing)
brightness() (in module biapy.data.generators.augmentors)
brightness_em() (in module biapy.data.generators.augmentors)
build_callbacks() (in module biapy.engine)
build_model() (in module biapy.models)
build_torchvision_model() (in module biapy.models)
C
calculate_z_filtering() (in module biapy.data.post_processing.post_processing)
calculate_zy_filtering() (in module biapy.data.post_processing.post_processing)
center_crop_single() (in module biapy.data.generators.augmentors)
ChannelAttention (class in biapy.models.rcan)
check_downsample_division() (in module biapy.utils.util)
check_generator_consistence() (in module biapy.data.generators)
check_masks() (in module biapy.utils.util)
check_value() (in module biapy.utils.util)
Classification_Workflow (class in biapy.engine.classification)
Config (class in biapy.config.config)
contrast() (in module biapy.data.generators.augmentors)
contrast_em() (in module biapy.data.generators.augmentors)
Conv_batchnorm (class in biapy.models.multiresunet)
create_gen() (in module biapy.data.post_processing.smooth_tiled_predictions)
create_plots() (in module biapy.utils.util)
create_test_augmentor() (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.utils.util)
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)
destroy_test_data() (biapy.engine.base_workflow.Base_Workflow method)
destroy_train_data() (biapy.engine.base_workflow.Base_Workflow method)
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)
dfcan_loss (class in biapy.engine.metrics)
dice_loss() (in module biapy.engine.metrics)
divide_images_on_classes() (in module biapy.utils.util)
do_save_wm() (in module biapy.utils.util)
draw_grid() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method)
(biapy.data.generators.single_base_data_generator.SingleBaseDataGenerator method)
E
EarlyStopping (class in biapy.utils.callbacks)
EDSR (class in biapy.models.edsr)
efficientnet() (in module biapy.models.efficientnet)
ensemble16_3d_predictions() (in module biapy.data.post_processing.post_processing)
ensemble8_2d_predictions() (in module biapy.data.post_processing.post_processing)
ensure_shape() (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)
evaluate() (in module biapy.engine.train_engine)
extract_3D_patch_with_overlap_yield() (in module biapy.data.data_3D_manipulation)
extract_patch_from_dataset() (in module biapy.engine.base_workflow)
F
fftshift2d() (in module biapy.models.dfcan)
find_neighbors() (in module biapy.data.post_processing.post_processing)
flush() (biapy.utils.misc.TensorboardLogger method)
foreground_percentage() (in module biapy.utils.util)
forward() (biapy.engine.metrics.dfcan_loss method)
(biapy.models.attention_unet.Attention_U_Net 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.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.seunet.SE_U_Net method)
(biapy.models.simple_cnn.simple_CNN method)
(biapy.models.unet.U_Net method)
(biapy.models.unetr.UNETR 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
get_cfg_defaults() (biapy.config.config.Config method)
get_checkpoint_path() (in module biapy.utils.misc)
get_data_normalization() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method)
(biapy.data.generators.single_base_data_generator.SingleBaseDataGenerator method)
get_grad_norm_() (in module biapy.utils.misc)
get_rank() (in module biapy.utils.misc)
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)
I
img_to_onehot_encoding() (in module biapy.utils.util)
init_devices() (in module biapy.utils.misc)
initialize_weights() (biapy.models.mae.MaskedAutoencoderViT method)
insert_patch_into_dataset() (in module biapy.engine.base_workflow)
instance_metrics (class in biapy.engine.metrics)
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_dist_avail_and_initialized() (in module biapy.utils.misc)
is_main_process() (in module biapy.utils.misc)
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
L1_wrapper (class in biapy.engine.metrics)
load_3d_data_classification() (in module biapy.data.data_3D_manipulation)
load_3D_efficient_files() (in module biapy.data.data_3D_manipulation)
load_3d_images_from_dir() (in module biapy.utils.util)
load_and_prepare_2D_train_data() (in module biapy.data.data_2D_manipulation)
load_and_prepare_3D_data() (in module biapy.data.data_3D_manipulation)
load_and_prepare_3D_efficient_format_data() (in module biapy.data.data_3D_manipulation)
load_ct_data_from_dir() (in module biapy.utils.util)
load_data_classification() (in module biapy.data.data_2D_manipulation)
load_data_from_dir() (in module biapy.utils.util)
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_state_dict() (biapy.utils.misc.NativeScalerWithGradNormCount method)
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)
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() (in module biapy.engine.metrics)
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)
merge_3D_data_with_overlap() (in module biapy.data.data_3D_manipulation)
merge_data_with_overlap() (in module biapy.data.data_2D_manipulation)
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.config
biapy.data
biapy.data.data_2D_manipulation
biapy.data.data_3D_manipulation
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.post_processing
biapy.data.post_processing.post_processing
biapy.data.post_processing.smooth_tiled_predictions
biapy.engine
biapy.engine.base_workflow
biapy.engine.classification
biapy.engine.denoising
biapy.engine.detection
biapy.engine.instance_seg
biapy.engine.metrics
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.dfcan
biapy.models.edsr
biapy.models.efficientnet
biapy.models.mae
biapy.models.multiresunet
biapy.models.rcan
biapy.models.resunet
biapy.models.seunet
biapy.models.simple_cnn
biapy.models.unet
biapy.models.unetr
biapy.models.vit
biapy.models.wdsr
biapy.utils.callbacks
biapy.utils.misc
biapy.utils.util
MSE_wrapper (class in biapy.engine.metrics)
MultiEpochsDataLoader (class in biapy.data.generators)
Multiresblock (class in biapy.models.multiresunet)
MultiResUnet (class in biapy.models.multiresunet)
N
n2v_loss_mse() (in module biapy.engine.metrics)
NativeScalerWithGradNormCount (class in biapy.utils.misc)
norm_X() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method)
norm_Y() (biapy.data.generators.pair_base_data_generator.PairBaseDataGenerator method)
normal_int() (in module biapy.engine.denoising)
normalize_stats() (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)
O
onehot_encoding_to_img() (in module biapy.utils.util)
order_dimensions() (in module biapy.utils.util)
P
pad_and_reflect() (in module biapy.utils.util)
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)
patchify() (biapy.models.mae.MaskedAutoencoderViT method)
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_img_with_overlap() (in module biapy.data.post_processing.smooth_tiled_predictions)
predict_img_with_smooth_windowing() (in module biapy.data.post_processing.smooth_tiled_predictions)
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)
print_post_processing_stats() (biapy.engine.base_workflow.Base_Workflow method)
print_stats() (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_patch() (biapy.engine.detection.Detection_Workflow method)
process_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_sample_by_chunks() (biapy.engine.base_workflow.Base_Workflow method)
proj_feat() (biapy.models.unetr.UNETR method)
R
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)
random_rotate_matrix() (in module biapy.data.generators.augmentors)
RCAB (class in biapy.models.dfcan)
(class in biapy.models.rcan)
rcan (class in biapy.models.rcan)
read_chunked_data() (in module biapy.utils.util)
remove_close_points() (in module biapy.data.post_processing.post_processing)
repare_large_blobs() (in module biapy.data.post_processing.post_processing)
ResGroup (class in biapy.models.dfcan)
resize_img() (in module biapy.data.generators.augmentors)
Respath (class in biapy.models.multiresunet)
ResUNet (class in biapy.models.resunet)
RG (class in biapy.models.rcan)
rotation() (in module biapy.data.generators.augmentors)
S
sample_coords() (in module biapy.engine.denoising)
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_img() (in module biapy.utils.util)
save_model() (in module biapy.utils.misc)
save_npy_files() (in module biapy.utils.util)
save_on_master() (in module biapy.utils.misc)
save_tif() (in module biapy.utils.util)
save_tif_pair_discard() (in module biapy.utils.util)
SE_U_Net (class in biapy.models.seunet)
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)
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)
SmoothedValue (class in biapy.utils.misc)
SR_convblock (class in biapy.models.edsr)
SR_upsampling (class in biapy.models.edsr)
SSIM_wrapper (class in biapy.engine.metrics)
state_dict() (biapy.utils.misc.NativeScalerWithGradNormCount method)
state_dict_key (biapy.utils.misc.NativeScalerWithGradNormCount attribute)
Super_resolution_Workflow (class in biapy.engine.super_resolution)
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_numpy_format() (in module biapy.utils.misc)
to_pytorch_format() (in module biapy.utils.misc)
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)
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)
UNETR (class in biapy.models.unetr)
unpatchify() (biapy.models.mae.MaskedAutoencoderViT method)
update() (biapy.utils.misc.MetricLogger method)
(biapy.utils.misc.SmoothedValue method)
(biapy.utils.misc.TensorboardLogger method)
update_dependencies() (biapy.config.config.Config method)
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)
voc_calculation() (in module biapy.engine.metrics)
voronoi_on_mask() (in module biapy.data.post_processing.post_processing)
W
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)
weighted_bce_dice_loss() (in module biapy.engine.metrics)
write_chunked_data() (in module biapy.utils.util)
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