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b/src/inference.py |
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import torch |
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import torch.nn as nn |
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import torch.nn.functional as Ftorch |
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from torch.utils.data import DataLoader |
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from tqdm import * |
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from models import * |
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from augmentation import * |
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from dataset import * |
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import glob |
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device = torch.device('cuda') |
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def predict(model, loader): |
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model.eval() |
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preds = [] |
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with torch.no_grad(): |
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for dct in tqdm(loader, total=len(loader)): |
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images = dct['images'].to(device) |
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# meta = dct["meta"].to(device) |
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pred = model(images) |
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pred = Ftorch.sigmoid(pred) |
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pred = pred.detach().cpu().numpy() |
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preds.append(pred) |
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preds = np.concatenate(preds, axis=0) |
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return preds |
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def get_best_checkpoints(checkpoint_dir, n_best=3, minimize_metric=True): |
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files = glob.glob(f"{checkpoint_dir}/checkpoints/best*.pth") |
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files = [file for file in files if not 'full' in file] |
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top_best_metrics = [] |
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for file in files: |
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ckp = torch.load(file) |
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valid_metric = ckp['valid_metrics']['loss'] |
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top_best_metrics.append((file, valid_metric)) |
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top_best_metrics = sorted( |
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top_best_metrics, |
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key=lambda x: x[1], |
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reverse=not minimize_metric |
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) |
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top_best_metrics = top_best_metrics[:n_best] |
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return top_best_metrics |
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def predict_test_tta_ckp(): |
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test_csv = "./csv/patient2_kfold/test.csv" |
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# test_root = "/data/stage_1_test_3w/" |
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# test_root = "/data/png/test_stage_1/adjacent-brain-cropped/" |
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# test_root = "/data/stage_1_test_3w/" |
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test_root = "/data/stage_1_test_images_jpg_preprocessing/" |
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image_type = 'jpg' |
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image_size = [512, 512] |
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backbone = "densenet169" |
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normalization = True |
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# fold = 2 |
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for fold in [0, 1, 2, 3, 4]: |
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# /logs/rsna/test/resnet50-anju-512-resume-0/checkpoints//train512.13.pth |
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scheme = f"{backbone}-mw-512-resume-{fold}" |
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log_dir = f"/logs/rsna/test/{scheme}/" |
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with_any = True |
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if with_any: |
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num_classes = 6 |
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target_cols = LABEL_COLS |
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else: |
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num_classes = 5 |
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target_cols = LABEL_COLS_WITHOUT_ANY |
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# test_preds = 0 |
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top_best_metrics = get_best_checkpoints(log_dir, n_best=1, minimize_metric=True) |
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test_preds = 0 |
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for best_metric in top_best_metrics: |
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checkpoint_path, checkpoint_metric = best_metric |
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print("*" * 50) |
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print(f"checkpoint: {checkpoint_path}") |
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print(f"Metric: {checkpoint_metric}") |
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model = CNNFinetuneModels( |
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model_name=backbone, |
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num_classes=num_classes, |
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pretrained=False |
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) |
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ckp = os.path.join(log_dir, f"checkpoints/best.pth") |
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checkpoint = torch.load(ckp) |
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model.load_state_dict(checkpoint['model_state_dict']) |
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model = nn.DataParallel(model) |
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model = model.to(device) |
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augs = test_tta(image_size, normalization) |
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for name, aug in augs.items(): |
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print("Augmentation: {}".format(name)) |
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test_dataset = RSNADataset( |
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csv_file=test_csv, |
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root=test_root, |
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with_any=with_any, |
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transform=aug, |
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mode="test", |
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image_type=image_type |
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) |
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test_loader = DataLoader( |
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dataset=test_dataset, |
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batch_size=64, |
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shuffle=False, |
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num_workers=8, |
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) |
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test_preds += predict(model, test_loader) / (len(augs) * len(top_best_metrics)) |
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os.makedirs(f"/logs/prediction/{scheme}", exist_ok=True) |
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np.save(f"/logs/prediction/{scheme}/test_{fold}_ckp_tta.npy", test_preds) |
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test_df = pd.read_csv(test_csv) |
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test_ids = test_df['sop_instance_uid'].values |
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ids = [] |
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labels = [] |
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for i, id in enumerate(test_ids): |
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if not "ID" in id: |
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id = "ID_" + id |
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pred = test_preds[i] |
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for j, target in enumerate(target_cols): |
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id_target = id + "_" + target |
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ids.append(id_target) |
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labels.append(pred[j]) |
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if not with_any: |
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id_target = id + "_" + "any" |
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ids.append(id_target) |
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labels.append(pred.max()) |
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submission_df = pd.DataFrame({ |
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'ID': ids, |
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'Label': labels |
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}) |
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submission_df.to_csv(f"/logs/prediction/{scheme}/{scheme}_ckp_tta.csv", index=False) |
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def predict_valid_tta_ckp(): |
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# test_root = "/data/png/train/adjacent-brain-cropped/" |
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# test_root = "/data/stage_1_train_3w/" |
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test_root = "/data/stage_1_test_images_jpg_preprocessing/" |
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image_type = 'jpg' |
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image_size = [512, 512] |
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backbone = "densenet169" |
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normalization = True |
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# fold = 2 |
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for fold in [0, 1, 2, 3, 4]: |
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test_csv = f"./csv/patient2_kfold/valid_{fold}.csv" |
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# /logs/rsna/test/resnet50-anju-512-resume-0/checkpoints//train512.13.pth |
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scheme = f"{backbone}-mw-512-resume-{fold}" |
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log_dir = f"/logs/rsna/test/{scheme}/" |
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with_any = True |
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if with_any: |
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num_classes = 6 |
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target_cols = LABEL_COLS |
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else: |
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num_classes = 5 |
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target_cols = LABEL_COLS_WITHOUT_ANY |
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# test_preds = 0 |
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top_best_metrics = get_best_checkpoints(log_dir, n_best=1, minimize_metric=True) |
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test_preds = 0 |
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for best_metric in top_best_metrics: |
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checkpoint_path, checkpoint_metric = best_metric |
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print("*" * 50) |
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print(f"checkpoint: {checkpoint_path}") |
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print(f"Metric: {checkpoint_metric}") |
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model = CNNFinetuneModels( |
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model_name=backbone, |
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num_classes=num_classes, |
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) |
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ckp = os.path.join(log_dir, f"checkpoints/best.pth") |
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checkpoint = torch.load(ckp) |
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model.load_state_dict(checkpoint['model_state_dict']) |
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model = nn.DataParallel(model) |
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model = model.to(device) |
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augs = test_tta(image_size, normalization) |
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for name, aug in augs.items(): |
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print("Augmentation: {}".format(name)) |
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test_dataset = RSNADataset( |
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csv_file=test_csv, |
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root=test_root, |
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with_any=with_any, |
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transform=aug, |
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mode="valid", |
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image_type=image_type |
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) |
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test_loader = DataLoader( |
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dataset=test_dataset, |
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batch_size=64, |
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shuffle=False, |
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num_workers=8, |
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) |
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test_preds += predict(model, test_loader) / (len(augs) * len(top_best_metrics)) |
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os.makedirs(f"/logs/prediction/{scheme}", exist_ok=True) |
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np.save(f"/logs/prediction/{scheme}/valid_{scheme}.npy", test_preds) |
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test_df = pd.read_csv(test_csv) |
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test_ids = test_df['sop_instance_uid'].values |
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ids = [] |
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labels = [] |
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for i, id in enumerate(test_ids): |
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if not "ID" in id: |
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id = "ID_" + id |
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pred = test_preds[i] |
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for j, target in enumerate(target_cols): |
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id_target = id + "_" + target |
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ids.append(id_target) |
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labels.append(pred[j]) |
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if not with_any: |
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id_target = id + "_" + "any" |
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ids.append(id_target) |
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labels.append(pred.max()) |
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submission_df = pd.DataFrame({ |
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'ID': ids, |
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'Label': labels |
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}) |
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submission_df.to_csv(f"/logs/prediction/{scheme}/valid_{scheme}.csv", index=False) |
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if __name__ == '__main__': |
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# predict_test() |
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predict_test_tta_ckp() |
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# predict_valid_tta_ckp() |