Index

A

all_classes (metrics_sequential.SequentialMetrics attribute) all_metrics (metrics_sequential.SequentialMetrics attribute)

Attention (class in model.dim3.trans_layers) attention_up_block (class in model.dim3.attention_unet_utils) AttentionBlock (class in model.dim3.attention_unet_utils)

B

backward() (model.dim3.nnformer.ContiguousGrad static method) BasicBlock (class in model.dim3.conv_layers) BasicLayer (class in model.dim3.medformer_utils) (class in model.dim3.nnformer) (class in model.dim3.swin_unetr)

BasicLayer_up (class in model.dim3.nnformer) BidirectionAttention (class in model.dim3.medformer_utils) BidirectionAttentionBlock (class in model.dim3.medformer_utils) Bottleneck (class in model.dim3.conv_layers)

C

calculate_features_networks module calculate_flops() (in module calculate_features_networks) calculate_params() (in module calculate_features_networks) check_gpu_memory() (in module utils)

concat_all_gather() (in module training.utils) configure_logger() (in module utils) configure_optimizers() (train.Net method) ContBatchNorm3d (class in model.dim3.vnet) ContiguousGrad (class in model.dim3.nnformer) ConvNormAct (class in model.dim3.conv_layers)

D

dataset (train_sequential.SequentialTrain attribute) Decoder (class in model.dim3.nnformer) DepthwiseSeparableConv (class in model.dim3.conv_layers) dimensions (metrics_sequential.SequentialMetrics attribute) (predict_sequential.SequentialPredictions attribute) (train_sequential.SequentialTrain attribute)

down_block (class in model.dim3.medformer_utils) (class in model.dim3.unet_utils) DownTransition (class in model.dim3.vnet)

E

ELUCons() (in module model.dim3.vnet) Encoder (class in model.dim3.nnformer)

estimate_memory_inference() (in module calculate_features_networks) exp_lr_scheduler_with_warmup() (in module training.utils)

F

file_name (metrics_sequential.SequentialMetrics attribute) filter_validation_results() (in module training.utils) final_patch_expanding (class in model.dim3.nnformer) forward() (model.dim3.attention_unet_utils.attention_up_block method) (model.dim3.attention_unet_utils.AttentionBlock method) (model.dim3.conv_layers.BasicBlock method) (model.dim3.conv_layers.Bottleneck method) (model.dim3.conv_layers.ConvNormAct method) (model.dim3.conv_layers.DepthwiseSeparableConv method) (model.dim3.medformer.MedFormer method) (model.dim3.medformer_utils.BasicLayer method) (model.dim3.medformer_utils.BidirectionAttention method) (model.dim3.medformer_utils.BidirectionAttentionBlock method) (model.dim3.medformer_utils.down_block method) (model.dim3.medformer_utils.inconv method) (model.dim3.medformer_utils.PatchMerging method) (model.dim3.medformer_utils.SemanticMapFusion method) (model.dim3.medformer_utils.SemanticMapGeneration method) (model.dim3.medformer_utils.up_block method) (model.dim3.nnformer.BasicLayer method) (model.dim3.nnformer.BasicLayer_up method) (model.dim3.nnformer.ContiguousGrad static method) (model.dim3.nnformer.Decoder method) (model.dim3.nnformer.Encoder method) (model.dim3.nnformer.final_patch_expanding method) (model.dim3.nnformer.Mlp method) (model.dim3.nnformer.nnFormer method) (model.dim3.nnformer.Patch_Expanding method) (model.dim3.nnformer.PatchEmbed method) (model.dim3.nnformer.PatchMerging method) (model.dim3.nnformer.project method) (model.dim3.nnformer.SwinTransformerBlock method) (model.dim3.nnformer.SwinTransformerBlock_kv method) (model.dim3.nnformer.WindowAttention method) (model.dim3.nnformer.WindowAttention_kv method) (model.dim3.nnformer_utils.NeuralNetwork method) (model.dim3.swin_unetr.BasicLayer method) (model.dim3.swin_unetr.PatchMerging method) (model.dim3.swin_unetr.PatchMergingV2 method) (model.dim3.swin_unetr.SwinTransformer method) (model.dim3.swin_unetr.SwinTransformerBlock method) (model.dim3.swin_unetr.SwinUNETR method) (model.dim3.swin_unetr.WindowAttention method) (model.dim3.trans_layers.Attention method) (model.dim3.trans_layers.LayerNorm method) (model.dim3.trans_layers.Mlp method) (model.dim3.trans_layers.TransformerBlock method) (model.dim3.unet.UNet method) (model.dim3.unet_utils.down_block method) (model.dim3.unet_utils.inconv method) (model.dim3.unet_utils.up_block method) (model.dim3.unetpp.UNetPlusPlus method) (model.dim3.unetr.UNETR method) (model.dim3.vnet.ContBatchNorm3d method) (model.dim3.vnet.DownTransition method) (model.dim3.vnet.InputTransition method) (model.dim3.vnet.LUConv method) (model.dim3.vnet.OutputTransition method) (model.dim3.vnet.UpTransition method) (model.dim3.vnet.VNet method) (train.Net method)

forward_part1() (model.dim3.swin_unetr.SwinTransformerBlock method) forward_part2() (model.dim3.swin_unetr.SwinTransformerBlock method)

G

get_act() (in module model.dim3.utils) get_block() (in module model.dim3.utils) get_device() (model.dim3.nnformer_utils.NeuralNetwork method) get_latest_run_version_ckpt_epoch_no() (in module utils) get_model() (in module model.utils)

get_norm() (in module model.dim3.utils) get_optimizer() (in module training.utils) get_parser() (in module calculate_features_networks) (in module train) gt_img_path (metrics_sequential.SequentialMetrics attribute) gt_lbl_path (metrics_sequential.SequentialMetrics attribute)

H

human_readable() (in module calculate_features_networks)

I

inconv (class in model.dim3.medformer_utils) (class in model.dim3.unet_utils) InitWeights_He (class in model.dim3.nnformer_utils)

InitWeights_XavierUniform (class in model.dim3.nnformer_utils) InputTransition (class in model.dim3.vnet) is_master() (in module utils)

L

LayerNorm (class in model.dim3.trans_layers) len_battery_test (predict_sequential.SequentialPredictions attribute) (train_sequential.SequentialTrain attribute) load_from() (model.dim3.swin_unetr.SwinTransformerBlock method) (model.dim3.swin_unetr.SwinUNETR method) (model.dim3.unetr.UNETR method)

log_evaluation_result() (in module training.utils) LUConv (class in model.dim3.vnet)

M

main() (in module calculate_features_networks) main_profile() (in module calculate_features_networks) MainModule (class in train) make_layer() (model.dim3.unetpp.UNetPlusPlus method) maybe_to_torch() (in module model.dim3.nnformer_utils) MedFormer (class in model.dim3.medformer) memory_profile() (in module calculate_features_networks) metrics_sequential module Mlp (class in model.dim3.nnformer) (class in model.dim3.trans_layers) model module model.dim3.attention_unet_utils module model.dim3.conv_layers module model.dim3.medformer module model.dim3.medformer_utils module model.dim3.nnformer module model.dim3.nnformer_utils module model.dim3.swin_unetr module model.dim3.trans_layers module model.dim3.unet module model.dim3.unet_utils module model.dim3.unetpp module model.dim3.unetr module

model.dim3.utils module model.dim3.vnet module model.utils module models_2d (metrics_sequential.SequentialMetrics attribute) (predict_sequential.SequentialPredictions attribute) (train_sequential.SequentialTrain attribute) models_3d (metrics_sequential.SequentialMetrics attribute) (predict_sequential.SequentialPredictions attribute) (train_sequential.SequentialTrain attribute) module calculate_features_networks metrics_sequential model model.dim3.attention_unet_utils model.dim3.conv_layers model.dim3.medformer model.dim3.medformer_utils model.dim3.nnformer model.dim3.nnformer_utils model.dim3.swin_unetr model.dim3.trans_layers model.dim3.unet model.dim3.unet_utils model.dim3.unetpp model.dim3.unetr model.dim3.utils model.dim3.vnet model.utils predict_sequential train train_sequential training training.utils utils multistep_lr_scheduler_with_warmup() (in module training.utils)

N

name_dataset (metrics_sequential.SequentialMetrics attribute) Net (class in train)

NeuralNetwork (class in model.dim3.nnformer_utils) nnFormer (class in model.dim3.nnformer) no_op (class in model.dim3.nnformer_utils)

O

on_test_epoch_end() (train.Net method) on_training_epoch_end() (train.Net method)

on_validation_epoch_end() (train.Net method) OutputTransition (class in model.dim3.vnet)

P

parse_memory_size() (in module calculate_features_networks) passthrough() (in module model.dim3.vnet) Patch_Expanding (class in model.dim3.nnformer) patch_size (model.dim3.swin_unetr.SwinUNETR attribute) PatchEmbed (class in model.dim3.nnformer) PatchMerging (class in model.dim3.medformer_utils) (class in model.dim3.nnformer) (class in model.dim3.swin_unetr) PatchMergingV2 (class in model.dim3.swin_unetr)

predict() (train.MainModule method) predict_2D() (model.dim3.nnformer_utils.SegmentationNetwork method) predict_3D() (model.dim3.nnformer_utils.SegmentationNetwork method) predict_3D_pseudo3D_2Dconv() (model.dim3.nnformer_utils.SegmentationNetwork method) predict_sequential module proj_feat() (model.dim3.unetr.UNETR method) proj_out() (model.dim3.swin_unetr.SwinTransformer method) project (class in model.dim3.nnformer)

R

rearrange1() (model.dim3.medformer_utils.BidirectionAttention method) (model.dim3.trans_layers.Attention method) rearrange2() (model.dim3.medformer_utils.BidirectionAttention method) (model.dim3.trans_layers.Attention method)

remove_wrap_arounds() (in module training.utils) root_path (metrics_sequential.SequentialMetrics attribute) run_model() (predict_sequential.SequentialPredictions static method) (train_sequential.SequentialTrain static method)

S

sample_stack() (in module utils) save_configure() (in module utils) save_nifti() (in module utils) SegmentationNetwork (class in model.dim3.nnformer_utils) SemanticMapFusion (class in model.dim3.medformer_utils) SemanticMapGeneration (class in model.dim3.medformer_utils) separate_number_and_unit() (in module calculate_features_networks) SequentialMetrics (class in metrics_sequential)

SequentialPredictions (class in predict_sequential) SequentialTrain (class in train_sequential) set_device() (model.dim3.nnformer_utils.NeuralNetwork method) softmax_helper() (in module model.dim3.nnformer_utils) SwinTransformer (class in model.dim3.swin_unetr) SwinTransformerBlock (class in model.dim3.nnformer) (class in model.dim3.swin_unetr) SwinTransformerBlock_kv (class in model.dim3.nnformer) SwinUNETR (class in model.dim3.swin_unetr)

T

test() (train.MainModule method) test_step() (train.Net method) time_profile() (in module calculate_features_networks) to_cuda() (in module model.dim3.nnformer_utils) train module train() (train.MainModule method)

train_sequential module training module training.utils module training_step() (train.Net method) TransformerBlock (class in model.dim3.trans_layers)

U

UNet (class in model.dim3.unet) UNetPlusPlus (class in model.dim3.unetpp) UNETR (class in model.dim3.unetr) unwrap_model_checkpoint() (in module training.utils) up_block (class in model.dim3.medformer_utils) (class in model.dim3.unet_utils)

update_ema_variables() (in module training.utils) UpTransition (class in model.dim3.vnet) utils module

V

validation_step() (train.Net method)

VNet (class in model.dim3.vnet)

W

window_partition() (in module model.dim3.nnformer) (in module model.dim3.swin_unetr) window_reverse() (in module model.dim3.nnformer) (in module model.dim3.swin_unetr)

WindowAttention (class in model.dim3.nnformer) (class in model.dim3.swin_unetr) WindowAttention_kv (class in model.dim3.nnformer) write_data_json() (in module calculate_features_networks)