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Functions74 in github.com/AIRMEC/HECTOR

⨍ Functions 74◇ Types & classes 13
↓ 4 callersMethod__init__
( self, input_feature_size=1024, precompression_layer=True, feature_size_comp
model.py:137
↓ 2 callersMethod_update_loss_scores
(self, loss_score, eval_loss, epoch)
utils.py:163
↓ 2 callersMethod_update_metrics_scores
(self, CI_score, metrics_score, epoch)
utils.py:169
↓ 2 callersFunctionget_survival_data_for_BS
(df, time_col_name, censorship_col_name='censorship')
utils.py:185
↓ 2 callersFunctionnll_loss
(hazards, S, Y, c, alpha=0.4, eps=1e-7)
utils_loss.py:45
↓ 1 callersMethod__init__
( self, input_feature_size=1024, precompression_layer=True, feature_size_comp
im4MEC.py:35
↓ 1 callersMethod_get_feature_path
(self, slide_id)
utils.py:41
↓ 1 callersFunctioncompute_surv_metrics_eval
( bins_values, all_survival_probs, all_risk_scores, train_BS, test_BS, years_of_in
utils.py:209
↓ 1 callersFunctionconstruct_polygon
(foreground_contours, hole_contours, min_area)
extract_features.py:253
↓ 1 callersFunctioncreate_tissue_mask
(wsi, seg_level, method='otsu')
extract_features.py:340
↓ 1 callersFunctioncreate_tissue_tiles
(wsi, tissue_mask_scaled, tile_size_microns, offsets_micron=None)
extract_features.py:369
↓ 1 callersFunctioncrop_rect_from_slide
(slide, rect)
extract_features.py:442
↓ 1 callersFunctiondefine_data_sampling
(train_split, val_split, method, workers)
utils.py:66
↓ 1 callersFunctiondetect_foreground
(contours, hierarchy)
extract_features.py:235
↓ 1 callersFunctionevaluate_model
(epoch, model, model_mol, device, loader, n_bins, writer, loss_fn, bins_values, train_BS, test_BS)
train.py:32
↓ 1 callersFunctionextract_features
(model, device, wsi, filtered_tiles, workers, out_size, batch_size, n_last_blocks, avgpool_patchtokens, depths
extract_features.py:555
↓ 1 callersFunctionextract_save_features
(args)
extract_features.py:576
↓ 1 callersMethodforward_attention
(self, h)
model.py:254
↓ 1 callersMethodforward_attention
(self, h)
im4MEC.py:88
↓ 1 callersMethodforward_fusion
(self, h1, h2, h3)
model.py:260
↓ 1 callersMethodforward_survival
(self, logits)
model.py:279
↓ 1 callersFunctiongenerate_tiles
(tile_width_pix, tile_height_pix, img_width, img_height, offsets=[(0, 0)])
extract_features.py:298
↓ 1 callersFunctionget_args_parser
()
train.py:411
↓ 1 callersFunctionget_args_parser
()
extract_features.py:28
↓ 1 callersFunctionget_bins_time_value
(df, n_bins, time_col_name, label_time_col_name='disc_label', censorship_col_name='censorship')
utils.py:198
↓ 1 callersFunctionget_lr
(optimizer)
utils.py:176
↓ 1 callersFunctionload_encoder_esVIT
(args, device)
encoders.py:10
↓ 1 callersFunctionmain
(args)
train.py:305
↓ 1 callersFunctionmake_tile_QC_fig
(tiles, slide, level, line_width_pix=1, extra_tiles=None)
extract_features.py:322
↓ 1 callersFunctionmask_to_polygons
Convert a mask ndarray (binarized image) to Multipolygons
extract_features.py:188
↓ 1 callersFunctionmergedpatch_gen
(features, coords, dist_threshold=4, corr_threshold = 0.6)
extract_features.py:496
↓ 1 callersFunctionprepare_datasets
(args)
train.py:265
↓ 1 callersFunctionprint_model
(model)
utils.py:180
↓ 1 callersFunctionrun_train_eval_loop
(train_loader, val_loader, loss_fn, hparams, run_id, BS_data, checkpoint_model_molecular)
train.py:149
↓ 1 callersFunctionsegment_tissue
(img)
extract_features.py:129
↓ 1 callersFunctionsegment_tissue_deconv_stain
Method 2: Tissue segmentation using stain deconvolution. Alternative to Otsu thresholding.
extract_features.py:145
↓ 1 callersFunctionset_seed
()
train.py:19
↓ 1 callersFunctiontrain_one_epoch
(epoch, model, model_mol, device, train_loader, optimizer, n_bins, writer, loss_fn)
train.py:81
Method__call__
(self, epoch, eval_loss, eval_cindex, eval_other_metrics, model, log_dir)
utils.py:127
Method__call__
(self, hazards, S, Y, c, alpha=None)
utils_loss.py:68
Method__getitem__
(self, idx)
utils.py:44
Method__getitem__
(self, idx)
extract_features.py:468
Method__init__
(self, base_encoder, pretrained)
encoders.py:103
Method__init__
(self, df, data_dir, input_feature_size, stage_class)
utils.py:35
Method__init__
Args: patience (int): How long to wait after last time validation loss improved. Default: 20
utils.py:102
Method__init__
(self, alpha=0.15)
utils_loss.py:65
Method__init__
(self, wsi, tiles, resize_to=224)
extract_features.py:450
Method__init__
(self, space)
extract_features.py:539
Method__init__
(self, L=1024, D=256, dropout=False, p_dropout_atn=0.25, n_classes=1)
model.py:11
Method__init__
(self, gate_h1, gate_h2, gate_h3, dim1_og, dim2_og, dim3_og, use_bilinear=[True,True,True], scale=[1,1,1], p_d
model.py:35
Method__init__
(self, dim_in, dim_out, act_layer=nn.ReLU, dropout=True, p_dropout_fc=0.25)
model.py:97
Method__init__
(self, taxonomy_in=3, embedding_dim=128, depth=1, act_fct='relu', dropout=True, p_dropout=0.25)
model.py:111
Method__init__
(self, L=1024, D=256, dropout=False, p_dropout_atn=0.25, n_classes=1)
im4MEC.py:11
Method__len__
(self)
utils.py:63
Method__len__
(self)
extract_features.py:465
Method_init_weights
(self, module)
model.py:248
Method_init_weights
(self, module)
im4MEC.py:82
Functioncollate
(batch)
utils.py:21
Functioncollate_features
(batch)
extract_features.py:490
Methodfit
(self, X)
extract_features.py:542
Methodforward
(self, x)
encoders.py:107
Methodforward
(self, x)
model.py:26
Methodforward
(self, x1, x2, x3)
model.py:68
Methodforward
(self, x)
model.py:104
Methodforward
(self, x)
model.py:131
Methodforward
(self, h, stage, h_mol)
model.py:288
Methodforward
(self, x)
im4MEC.py:26
Methodforward
(self, h)
im4MEC.py:94
Functionload_encoder_resnet
(backbone, checkpoint_file, use_imagenet_weights, device)
encoders.py:98
Methodquery
(self, vector, topn)
extract_features.py:550
Methodsave_checkpoint
(self, model, log_dir, epoch)
utils.py:157
Functionseed_worker
(worker_id)
train.py:27
Functionseed_worker
(worker_id)
utils.py:16
Functiontile_is_not_empty
(tile, threshold_white=20)
extract_features.py:424