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b/evaluate.py |
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import argparse |
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import torch |
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from torch.utils.data import DataLoader |
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import pandas as pd |
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import os |
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import numpy as np |
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os.environ['KMP_DUPLICATE_LIB_OK']='True' |
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from dataset import LoadDataset |
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from model import InferenceNet, ECGnet |
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from utils import visualize_two_PC, ECG_visual_two, visualize_PC_with_twolabel_rotated |
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from loss import calculate_Dice, evaluate_pointcloud, calculate_inference_loss, calculate_reconstruction_loss |
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def evaluate(args): |
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DEVICE = torch.device('cuda:0') if torch.cuda.is_available() else torch.device('cpu') |
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test_dataset = LoadDataset(path=args.partial_root, num_input=args.num_input, split='test') |
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test_dataloader = DataLoader(test_dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) |
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# network = ECGnet(in_ch=args.in_ch, out_ch=args.out_ch, num_input=args.num_input, z_dims=args.z_dims) |
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network = InferenceNet(in_ch=args.in_ch, out_ch=args.out_ch, num_input=args.num_input, z_dims=args.z_dims) |
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network.load_state_dict(torch.load('log/net_model.pkl')) |
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network.to(DEVICE) |
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Dice_Scar, Dice_BZ = [], [] |
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precision_Scar, precision_BZ = [], [] |
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recall_Scar, recall_BZ = [], [] |
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f1_score_Scar, f1_score_BZ = [], [] |
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roc_auc_Scar, roc_auc_BZ = [], [] |
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pre_MI_size_Scar, pre_MI_size_BZ = [], [] |
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gd_MI_size_Scar, gd_MI_size_BZ = [], [] |
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MI_center_dist = [] |
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MI_type_list = [] |
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AHA_loc_score_list = [] |
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recon_geo_list, recon_ECG_list = [], [] |
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# testing: evaluate the mean loss |
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network.eval() |
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with torch.no_grad(): |
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for i, data in enumerate(test_dataloader, 1): |
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partial_input, ECG_input, gt_MI, partial_input_coarse, MI_type = data |
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partial_input, ECG_input, gt_MI = partial_input.to(DEVICE), ECG_input.to(DEVICE), gt_MI.to(DEVICE) |
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partial_input_coarse = partial_input_coarse.to(DEVICE) |
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partial_input = partial_input.permute(0, 2, 1) |
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y_MI, y_coarse, y_detail, y_ECG, mu, log_var = network(partial_input[:, 0:7, :], ECG_input) |
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loss_geo, loss_signal = calculate_reconstruction_loss(y_coarse, y_detail, partial_input_coarse, partial_input, y_ECG, ECG_input) |
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Dice = calculate_Dice(y_MI, gt_MI, num_classes=3) |
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precision, recall, f1_score, roc_auc, MI_size_pre, MI_size_gd, center_distance, AHA_loc_score = evaluate_pointcloud(y_MI, gt_MI, partial_input) |
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Dice_Scar.append(Dice[1].cpu().detach().numpy()) |
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Dice_BZ.append(Dice[2].cpu().detach().numpy()) |
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precision_Scar.append(precision[1]) |
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precision_BZ.append(precision[2]) |
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recall_Scar.append(recall[1]) |
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recall_BZ.append(recall[2]) |
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# f1_score_Scar.append(f1_score[1]) |
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# f1_score_BZ.append(f1_score[2]) |
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# roc_auc_Scar.append(roc_auc[1]) |
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# roc_auc_BZ.append(roc_auc[2]) |
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pre_MI_size_Scar.append(MI_size_pre[1]) |
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pre_MI_size_BZ.append(MI_size_pre[2]) |
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gd_MI_size_Scar.append(MI_size_gd[1]) |
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gd_MI_size_BZ.append(MI_size_gd[2]) |
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MI_center_dist.append(center_distance) |
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AHA_loc_score_list.append(AHA_loc_score) |
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recon_geo_list.append(loss_geo.cpu().detach().numpy()) |
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recon_ECG_list.append(loss_signal.cpu().detach().numpy()) |
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MI_type_list.append(MI_type[0]) |
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visual_check = False |
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if visual_check: |
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gd_ECG = ECG_input[0].cpu().detach().numpy() |
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y_ECG = y_ECG[0].cpu().detach().numpy() |
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ECG_visual_two(y_ECG, gd_ECG) |
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y_predict = y_MI[0].cpu().detach().numpy() |
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y_gd = gt_MI[0].cpu().detach().numpy() |
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x_input = partial_input[0].cpu().detach().numpy() |
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y_predict_argmax = np.argmax(y_predict, axis=0) |
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y_output = y_detail.permute(0, 2, 1)[0].cpu().detach().numpy() |
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visualize_PC_with_twolabel_rotated(x_input[0:3, 0:args.num_input].transpose(), y_predict_argmax, y_gd, filename='RNmap_gd_pre.pdf') |
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visualize_two_PC(x_input[0:3, 0:args.num_input].transpose(), y_output[0:3, 0:args.num_input].transpose(), y_gd, filename='PC_recon.pdf') |
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list = {'MI_type': MI_type_list, 'Dice_Scar': Dice_Scar, 'Dice_BZ': Dice_BZ, 'precision_Scar': precision_Scar, 'precision_BZ': precision_BZ, |
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'recall_Scar': recall_Scar, 'recall_BZ': recall_BZ, |
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'pre_MI_size_Scar': pre_MI_size_Scar, 'pre_MI_size_BZ': pre_MI_size_BZ, |
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'gd_MI_size_Scar': gd_MI_size_Scar, 'gd_MI_size_BZ': gd_MI_size_BZ |
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, 'MI_center_dist': MI_center_dist, 'AHA_loc_score': AHA_loc_score_list |
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, 'recon_geo': recon_geo_list, 'recon_ECG': recon_ECG_list} |
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df = pd.DataFrame(list) |
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df.to_csv('MI_inference_results_sample4.csv', encoding='gbk', index=False) |
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print('Lei, well done!') |
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if __name__ == "__main__": |
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parser = argparse.ArgumentParser() |
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parser.add_argument('--partial_root', type=str, default='./Big_data_inference/meta_data/UKB_clinical_data/') |
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parser.add_argument('--model', type=str, default='log/net_model.pkl') #'log/net_model.pkl' |
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parser.add_argument('--in_ch', type=int, default=3+4) # coordinate dimension + label index |
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parser.add_argument('--out_ch', type=int, default=3) # scar, BZ, normal |
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parser.add_argument('--z_dims', type=int, default=16) |
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parser.add_argument('--num_input', type=int, default=1024*4) |
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parser.add_argument('--batch_size', type=int, default=1) |
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parser.add_argument('--alpha', type=float, default=0.1) |
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parser.add_argument('--beta', type=float, default=1e-2) |
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parser.add_argument('--lamda', type=float, default=1) |
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parser.add_argument('--base_lr', type=float, default=1e-5) #5e-5 |
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parser.add_argument('--lr_decay_steps', type=int, default=50) |
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parser.add_argument('--lr_decay_rate', type=float, default=0.5) |
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parser.add_argument('--weight_decay', type=float, default=1e-6) #1e-3 |
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parser.add_argument('--epochs', type=int, default=500) |
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parser.add_argument('--num_workers', type=int, default=1) |
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parser.add_argument('--log_dir', type=str, default='log') |
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args = parser.parse_args() |
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evaluate(args) |
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